diff --git a/Source/mesquite/Mesquite.java b/Source/mesquite/Mesquite.java
index 4ca36fde1..42cd234a0 100644
--- a/Source/mesquite/Mesquite.java
+++ b/Source/mesquite/Mesquite.java
@@ -37,24 +37,24 @@ public class Mesquite extends MesquiteTrunk
 {
 	/*.................................................................................................................*/
 	public String getCitation() {
-		return "Maddison, W.P. & D.R. Maddison. 2018. Mesquite: A modular system for evolutionary analysis.  Version 3.6.  http://www.mesquiteproject.org";
+		return "Maddison, W.P. & D.R. Maddison. 2019. Mesquite: A modular system for evolutionary analysis.  Version 3.61.  http://www.mesquiteproject.org";
 	}
 	/*.................................................................................................................*/
 	public String getVersion() {
-		return "3.6";
+		return "3.61";
 	}
 
 	/*.................................................................................................................*/
 	public int getVersionInt() {
-		return 360;
+		return 361;
 	}
 	/*.................................................................................................................*/
 	public double getMesquiteVersionNumber(){
-		return 3.6;
+		return 3.61;
 	}
 	/*.................................................................................................................*/
 	public String getDateReleased() {
-		return "December 2018"; //"April 2007";
+		return "December 2019"; //"April 2007";
 	}
 	/*.................................................................................................................*/
 	public boolean isPrerelease(){
@@ -380,7 +380,7 @@ else if (prefsFile.exists() || prefsFileXML.exists()) {
 		String logInitString = "Mesquite version " + getMesquiteVersion() + getBuildVersion() + "\n";
 		if (StringUtil.notEmpty(MesquiteModule.getSpecialVersion()))
 			logInitString  +="  " + MesquiteModule.getSpecialVersion()+ "\n";
-		logInitString  += ("Copyright (c) 1997-2018 W. Maddison and D. Maddison\n");
+		logInitString  += ("Copyright (c) 1997-2019 W. Maddison and D. Maddison\n");
 		logInitString  += "The basic Mesquite package (class library and basic modules) is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License. "
 				+ "  Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.  For details on license and "
 				+ "lack of warranty see the GNU Lesser General Public License by selecting \"Display License\" from the Window menu or at www.gnu.org\n"
diff --git a/Source/mesquite/align/AlignDNAToProtein/AlignDNAToProtein.java b/Source/mesquite/align/AlignDNAToProtein/AlignDNAToProtein.java
index 4bfbb9eb6..9dc72173e 100644
--- a/Source/mesquite/align/AlignDNAToProtein/AlignDNAToProtein.java
+++ b/Source/mesquite/align/AlignDNAToProtein/AlignDNAToProtein.java
@@ -70,7 +70,7 @@ public boolean forceAlignment(DNAData dnaData, ProteinData proteinData, int it)
 		int numBases = dnaData.getNumberApplicableInTaxon(it, true);
 		int numAAs = proteinData.getNumberApplicableInTaxon(it, true);
 		if (numAAs*3!= numBases) {
-			logln("Number of nucleotides in sequence does not correspond to number of amino acids in protein sequence (taxon " + it+1 + ")");
+			logln("Number of nucleotides (\" + numBases + \") in sequence does not correspond to number of amino acids  (\" + numAAs + \") in protein sequence (taxon " + (it+1) + ")");
 			return false;
 		}
 		
diff --git a/Source/mesquite/align/MuscleAlign/MuscleAlign.java b/Source/mesquite/align/MuscleAlign/MuscleAlign.java
index 759fd5979..e2e245907 100644
--- a/Source/mesquite/align/MuscleAlign/MuscleAlign.java
+++ b/Source/mesquite/align/MuscleAlign/MuscleAlign.java
@@ -40,7 +40,7 @@ public boolean showCitation() {
 	}
 	/*.................................................................................................................*/
 	public String getCitation()  {
-		return "Please remember to cite the version of Muscle you used.";
+		return "Please remember to cite the version of MUSCLE you used.";
 	}
 	/*.................................................................................................................*/
 	public boolean isSubstantive(){
@@ -52,11 +52,11 @@ public boolean isPrerelease(){
 	}
 	/*.................................................................................................................*/
 	public String getName() {
-		return "Muscle Align";
+		return "MUSCLE Align";
 	}
 	/*.................................................................................................................*/
 	public String getNameForMenuItem() {
-		return "Muscle Align...";
+		return "MUSCLE Align...";
 	}
 	/*.................................................................................................................*/
 	/** returns an explanation of what the module does.*/
@@ -65,9 +65,13 @@ public String getExplanation() {
 	}
 	
 	public String getProgramName(){
-		 return "Muscle";
+		 return "MUSCLE";
 	 }
-	
+	/*.................................................................................................................*/
+	public String getHelpURL(){
+		return "http://www.drive5.com/muscle/manual/";
+	}
+
 	/*.................................................................................................................*/
 	public String getHelpString() {
 	  String s =  " In the Muscle Options field, place any Muscle options you wish to use.  For example, if you wished to change the"
diff --git a/Source/mesquite/align/lib/AlignUtil.java b/Source/mesquite/align/lib/AlignUtil.java
index 1ef62db39..0eff6f03a 100644
--- a/Source/mesquite/align/lib/AlignUtil.java
+++ b/Source/mesquite/align/lib/AlignUtil.java
@@ -590,7 +590,7 @@ public static boolean integrateAlignment(long[][] alignedMatrix, MolecularData d
 				data.setSelected(i, true);
 
 		}
-		MesquiteTrunk.mesquiteTrunk.logln("Alignment completed.");
+		MesquiteTrunk.mesquiteTrunk.logln("Alignment completed for " + data.getName());
 		data.removeCharactersThatAreEntirelyGaps(icStart, icEnd, true);  // added 1 June 2016
 
 		return true;
diff --git a/Source/mesquite/align/lib/ExternalSequenceAligner.java b/Source/mesquite/align/lib/ExternalSequenceAligner.java
index 05be6ce47..9c416b78f 100644
--- a/Source/mesquite/align/lib/ExternalSequenceAligner.java
+++ b/Source/mesquite/align/lib/ExternalSequenceAligner.java
@@ -450,15 +450,15 @@ else if (!(firstTaxon==0 && lastTaxon==matrix.getNumTaxa())) {  // we are doing
 				if (success) {
 					for (int i=1; i<alignedTaxa.getNumTaxa() ; i++) {
 						for (int j= i-1; j>=0 && j+1<keys.length && keys[j]>keys[j+1]; j--) {
-							alignedTaxa.swapParts(j, j+1);
+							alignedTaxa.swapParts(j, j+1, false);
 							int kj = keys[j];
 							keys[j] = keys[j+1];
 							keys[j+1] = kj;
 							//alignedData.swapTaxa(j, j+1);
 						}
 					}
+					alignedTaxa.notifyListeners(this, new Notification(MesquiteListener.PARTS_MOVED));
 					alignedData.changed(this, alignedTaxa, new Notification(MesquiteListener.PARTS_MOVED));
-
 					if (alignedData instanceof MolecularData){
 						aligned = new long[alignedData.getNumChars()][originalTaxa.getNumTaxa()];
 						for (int ic = 0; ic<alignedData.getNumChars(); ic++)
diff --git a/Source/mesquite/ancstates/TraceCharOverTrees/TraceCharOverTrees.java b/Source/mesquite/ancstates/TraceCharOverTrees/TraceCharOverTrees.java
index 5da13590d..1f03f5a24 100644
--- a/Source/mesquite/ancstates/TraceCharOverTrees/TraceCharOverTrees.java
+++ b/Source/mesquite/ancstates/TraceCharOverTrees/TraceCharOverTrees.java
@@ -921,7 +921,7 @@ else if (!tempCharStates.frequenciesExist() && mode == AVERAGE_FREQUENCIES) {
 				}
 				if (showNodeAbsent){
 					extraNames[NODE_ABSENT] = "Node Absent";
-					extraColors.setColor(NODE_ABSENT,Color.red);
+					extraColors.setColor(NODE_ABSENT,ColorDistribution.veryLightBlue);
 				}
 				charStates.setExtraFrequencyNames(extraNames);
 				charStates.setExtraFrequencyColors(extraColors);
diff --git a/Source/mesquite/basic/VoucherInfoFromFlexTable/VoucherInfoFromFlexTable.java b/Source/mesquite/basic/VoucherInfoFromFlexTable/VoucherInfoFromFlexTable.java
index b05f8aa14..2f204bd65 100644
--- a/Source/mesquite/basic/VoucherInfoFromFlexTable/VoucherInfoFromFlexTable.java
+++ b/Source/mesquite/basic/VoucherInfoFromFlexTable/VoucherInfoFromFlexTable.java
@@ -1 +1 @@
-/* Mesquite source code.  Copyright 2005 and onward, David Maddison and Wayne Maddison.

Disclaimer:  The Mesquite source code is lengthy and we are few.  There are no doubt inefficiencies and goofs in this code. 
The commenting leaves much to be desired. Please approach this source code with the spirit of helping out.
Perhaps with your help we can be more than a few, and make Mesquite better.

Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.
Mesquite's web site is http://mesquiteproject.org

This source code and its compiled class files are free and modifiable under the terms of 
GNU Lesser General Public License.  (http://www.gnu.org/copyleft/lesser.html)
 */


package mesquite.basic.VoucherInfoFromFlexTable; 


import mesquite.lib.*;
import java.util.Vector;


/* ======================================================================== */

public class  VoucherInfoFromFlexTable extends OTUIDCodeInfoSource {
	Vector tables, paths, lastModified;
	boolean warned = false;
	/*.................................................................................................................*/
	public boolean startJob(String arguments, Object condition, boolean hiredByName) {
		paths = new Vector();
		tables = new Vector();
		lastModified = new Vector();
		return true;
	}
	
	/*.................................................................................................................*/
	private String getPath(String databaseID){
		String where = null;
		if (databaseID.indexOf(":")<0)
			where = databaseID;
		else
			where = databaseID.substring(databaseID.indexOf(":")+1, databaseID.length());
		if (!warned && StringUtil.blank(where)) {
			MesquiteMessage.warnProgrammer("Path of voucher info file is empty; databaseID = " + databaseID);
			warned = true;
		}
		return where;
	}
	/*.................................................................................................................*/
	private String getDBID(String databaseID){
		String which = null;
		if (databaseID.indexOf(":")<0)
			which = databaseID;
		else
			which = databaseID.substring(0, databaseID.indexOf(":"));
		if (!warned && StringUtil.blank(which)) {
			MesquiteMessage.warnProgrammer("DBID of voucher info file is empty; databaseID = " + databaseID);
			warned = true;
		}
		return which;
	}
	/** Looks in the paths Vector to see if it can find the path passed as an argument.   If so, and if the last modified time of the file
	 * at that path has not changed, then this method returns the index of the path. If so, but the last modified time of the file has changed,
	 * then this method returns one less than the negative of the index.  If no such path was found, the method returns MesquiteInteger.unassigned. */
	private int findPath(String path){
		if (path == null)
			return MesquiteInteger.unassigned;
		for (int i=0; i<paths.size(); i++)
			if (path.equals(paths.elementAt(i))) {
				MesquiteLong lastModifiedTime = (MesquiteLong)lastModified.elementAt(i);
				if (lastModifiedTime.getValue()!=MesquiteFile.fileOrDirectoryLastModified(path)) {  // has been modified
					return -i-1;  // return negative if i; subtract 1 so that 0 turns into -1
				}
				return i;
			}
		return MesquiteInteger.unassigned;
	}
	private int findRow(String[][] table, String id){
		for (int i=0; i<table.length; i++){
			if (table[i] != null && table[i].length>0 && id.equalsIgnoreCase(table[i][0]))
				return i;
			
		}
		return -1;
	}
	private VoucherInfoFromOTUIDDB makeInfo(String[][] table, int row){
		
		if (table == null || row>= table.length)
			return null;

		VoucherInfoFromOTUIDDB vi = new VoucherInfoFromOTUIDDB();
		String[] line = table[0];  		// cycle through first row to get field names
		for (int i = 1; i<line.length; i++)  //start at 1 as we don't want to include the code
			vi.addElement(line[i]);
		
		line = table[row];
		if (line == null || line.length == 0)
			return null;
		for (int i = 1; i<line.length; i++)  //start at 1 as we don't want to include the code
			vi.setFieldValue(i-1, line[i]);   //index is i-1 as we skipped over the first one
		return vi;
	}
	/*.................................................................................................................*/
//	String voucherID, String species, String latLong, String locality, String note, String collectionDate
	
	public VoucherInfoFromOTUIDDB getVoucherInfo(String databaseID, String id){
		if (!handlesDatabase(databaseID))
			return null;
		String path = getPath(databaseID);
		if (path == null)
			return null;
		int i = findPath(path);
		String[][] table = null;
		if (i==MesquiteInteger.unassigned){  // didn't find it
			table = MesquiteFile.getTabDelimitedTextFile(path, false);
			if (table != null){
				paths.addElement(path);
				tables.addElement(table);
				lastModified.addElement(new MesquiteLong(MesquiteFile.fileOrDirectoryLastModified(path)));  // store last modified
			}
		} else if (i<0) {  // did find it, but last modified date has changed.
			table = MesquiteFile.getTabDelimitedTextFile(path, false);
			if (table != null){
				i=-i-1; // need to take negative and subract 1
				tables.setElementAt(table, i);
				lastModified.setElementAt(new MesquiteLong(MesquiteFile.fileOrDirectoryLastModified(path)), i);  // reset last modified
			}
		} else
			table = (String[][]) tables.elementAt(i);
		if (table == null)
			return null;
		int whichRow = findRow(table, id);
		if (whichRow<0)
			return null;
		return makeInfo(table, whichRow);
	}
	/*.................................................................................................................*/
	public boolean handlesDatabase(String databaseID){
		if (databaseID == null)
			return false;
		String which = getDBID(databaseID);
		return "tdt".equalsIgnoreCase(which);
	}
	
	/*.................................................................................................................*/
	public String getName() {
		return "Voucher Info from Flexible Table";
	}
	/*.................................................................................................................*/
	public boolean isPrerelease(){
		return false;  
	}
	/*.................................................................................................................*/
	/** returns the version number at which this module was first released.  If 0, then no version number is claimed.  If a POSITIVE integer
	 * then the number refers to the Mesquite version.  This should be used only by modules part of the core release of Mesquite.
	 * If a NEGATIVE integer, then the number refers to the local version of the package, e.g. a third party package*/
	public int getVersionOfFirstRelease(){
		return -1;  
	}
	/*.................................................................................................................*/
	/** returns whether this module is requesting to appear as a primary choice */
	public boolean requestPrimaryChoice(){
		return true;  
	}
	
	/*.................................................................................................................*/
	/** returns an explanation of what the module does.*/
	public String getExplanation() {
		return "Supplies voucher information from a flexible tab-delimited table in a text file." ;
	}
}


\ No newline at end of file
+/* Mesquite source code.  Copyright 2005 and onward, David Maddison and Wayne Maddison.

Disclaimer:  The Mesquite source code is lengthy and we are few.  There are no doubt inefficiencies and goofs in this code. 
The commenting leaves much to be desired. Please approach this source code with the spirit of helping out.
Perhaps with your help we can be more than a few, and make Mesquite better.

Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.
Mesquite's web site is http://mesquiteproject.org

This source code and its compiled class files are free and modifiable under the terms of 
GNU Lesser General Public License.  (http://www.gnu.org/copyleft/lesser.html)
 */


package mesquite.basic.VoucherInfoFromFlexTable; 


import mesquite.lib.*;
import java.util.Vector;


/* ======================================================================== */

public class  VoucherInfoFromFlexTable extends OTUIDCodeInfoSource {
	Vector tables, paths, lastModified;
	boolean warned = false;
	/*.................................................................................................................*/
	public boolean startJob(String arguments, Object condition, boolean hiredByName) {
		paths = new Vector();
		tables = new Vector();
		lastModified = new Vector();
		return true;
	}
	
	/*.................................................................................................................*/
	private String getPath(String databaseID){
		String where = null;
		if (databaseID.indexOf(":")<0)
			where = databaseID;
		else
			where = databaseID.substring(databaseID.indexOf(":")+1, databaseID.length());
		where = StringUtil.stripLeadingWhitespace(where);
		if (where.startsWith("/")) //not local path
			;
		else if (where.startsWith("\\")) //not local path
			;
		else { // local path
			MesquiteFile fi = getProject().getHomeFile();
			if (fi != null && fi.isLocal()) {
				String filePath = fi.getDirectoryName();
				where = filePath+where;
			}
			
		}
		if (!warned && StringUtil.blank(where)) {
			MesquiteMessage.warnProgrammer("Path of voucher info file is empty; databaseID = " + databaseID);
			warned = true;
		}
		return where;
	}
	/*.................................................................................................................*/
	private String getDBID(String databaseID){
		String which = null;
		if (databaseID.indexOf(":")<0)
			which = databaseID;
		else
			which = databaseID.substring(0, databaseID.indexOf(":"));
		if (!warned && StringUtil.blank(which)) {
			MesquiteMessage.warnProgrammer("DBID of voucher info file is empty; databaseID = " + databaseID);
			warned = true;
		}
		return which;
	}
	/** Looks in the paths Vector to see if it can find the path passed as an argument.   If so, and if the last modified time of the file
	 * at that path has not changed, then this method returns the index of the path. If so, but the last modified time of the file has changed,
	 * then this method returns one less than the negative of the index.  If no such path was found, the method returns MesquiteInteger.unassigned. */
	private int findPath(String path){
		if (path == null)
			return MesquiteInteger.unassigned;
		for (int i=0; i<paths.size(); i++)
			if (path.equals(paths.elementAt(i))) {
				MesquiteLong lastModifiedTime = (MesquiteLong)lastModified.elementAt(i);
				if (lastModifiedTime.getValue()!=MesquiteFile.fileOrDirectoryLastModified(path)) {  // has been modified
					return -i-1;  // return negative if i; subtract 1 so that 0 turns into -1
				}
				return i;
			}
		return MesquiteInteger.unassigned;
	}
	private int findRow(String[][] table, String id){
		for (int i=0; i<table.length; i++){
			if (table[i] != null && table[i].length>0 && id.equalsIgnoreCase(table[i][0]))
				return i;
			
		}
		return -1;
	}
	private VoucherInfoFromOTUIDDB makeInfo(String[][] table, int row){
		
		if (table == null || row>= table.length)
			return null;

		VoucherInfoFromOTUIDDB vi = new VoucherInfoFromOTUIDDB();
		String[] line = table[0];  		// cycle through first row to get field names
		for (int i = 1; i<line.length; i++)  //start at 1 as we don't want to include the code
			vi.addElement(line[i]);
		
		line = table[row];
		if (line == null || line.length == 0)
			return null;
		for (int i = 1; i<line.length; i++)  //start at 1 as we don't want to include the code
			vi.setFieldValue(i-1, line[i]);   //index is i-1 as we skipped over the first one
		return vi;
	}
	/*.................................................................................................................*/
//	String voucherID, String species, String latLong, String locality, String note, String collectionDate
	
	public VoucherInfoFromOTUIDDB getVoucherInfo(String databaseID, String id){
		if (!handlesDatabase(databaseID))
			return null;
		String path = getPath(databaseID);
		if (path == null)
			return null;
		int i = findPath(path);
		String[][] table = null;
		if (i==MesquiteInteger.unassigned){  // didn't find it
			table = MesquiteFile.getTabDelimitedTextFile(path, false);
			if (table != null){
				paths.addElement(path);
				tables.addElement(table);
				lastModified.addElement(new MesquiteLong(MesquiteFile.fileOrDirectoryLastModified(path)));  // store last modified
			}
		} else if (i<0) {  // did find it, but last modified date has changed.
			table = MesquiteFile.getTabDelimitedTextFile(path, false);
			if (table != null){
				i=-i-1; // need to take negative and subract 1
				tables.setElementAt(table, i);
				lastModified.setElementAt(new MesquiteLong(MesquiteFile.fileOrDirectoryLastModified(path)), i);  // reset last modified
			}
		} else
			table = (String[][]) tables.elementAt(i);
		if (table == null)
			return null;
		int whichRow = findRow(table, id);
		if (whichRow<0)
			return null;
		return makeInfo(table, whichRow);
	}
	/*.................................................................................................................*/
	public boolean handlesDatabase(String databaseID){
		if (databaseID == null)
			return false;
		String which = getDBID(databaseID);
		return "tdt".equalsIgnoreCase(which);
	}
	
	/*.................................................................................................................*/
	public String getName() {
		return "Voucher Info from Flexible Table";
	}
	/*.................................................................................................................*/
	public boolean isPrerelease(){
		return false;  
	}
	/*.................................................................................................................*/
	/** returns the version number at which this module was first released.  If 0, then no version number is claimed.  If a POSITIVE integer
	 * then the number refers to the Mesquite version.  This should be used only by modules part of the core release of Mesquite.
	 * If a NEGATIVE integer, then the number refers to the local version of the package, e.g. a third party package*/
	public int getVersionOfFirstRelease(){
		return -1;  
	}
	/*.................................................................................................................*/
	/** returns whether this module is requesting to appear as a primary choice */
	public boolean requestPrimaryChoice(){
		return true;  
	}
	
	/*.................................................................................................................*/
	/** returns an explanation of what the module does.*/
	public String getExplanation() {
		return "Supplies voucher information from a flexible tab-delimited table in a text file." ;
	}
}


\ No newline at end of file
diff --git a/Source/mesquite/categ/ProportionUniqueStates/ProportionUniqueStates.java b/Source/mesquite/categ/ProportionUniqueStates/ProportionUniqueStates.java
index 8817b993b..931270c50 100644
--- a/Source/mesquite/categ/ProportionUniqueStates/ProportionUniqueStates.java
+++ b/Source/mesquite/categ/ProportionUniqueStates/ProportionUniqueStates.java
@@ -162,7 +162,7 @@ public void employeeParametersChanged(MesquiteModule employee, MesquiteModule so
 	}
 	/*.................................................................................................................*/
 	public String getVeryShortName() {
-		if (observedStates != null && getProject().getNumberCharMatricesVisible()>1){
+		if (observedStates != null && getProject() != null && getProject().getNumberCharMatricesVisible()>1){
 			CharacterData d = observedStates.getParentData();
 			if (d != null && d.getName()!= null) {
 				String n =  d.getName();
diff --git a/Source/mesquite/categ/lib/CategoricalData.java b/Source/mesquite/categ/lib/CategoricalData.java
index efca112b0..64b89ec04 100644
--- a/Source/mesquite/categ/lib/CategoricalData.java
+++ b/Source/mesquite/categ/lib/CategoricalData.java
@@ -545,12 +545,12 @@ public  boolean swapAssociated(int first, int second){
 		if (second<0 || second >= numChars)
 			return false;
 
-		return super.swapParts(first,second);
+		return super.swapParts(first,second, true);
 
 	}
 	/*..........................................  CategoricalData  ..................................................*/
 	/**swaps characters first and second*/
-	public  boolean swapParts(int first, int second){
+	public  boolean swapParts(int first, int second, boolean notify){
 		if (first<0 || first >= numChars)
 			return false;
 		if (second<0 || second >= numChars)
@@ -564,7 +564,7 @@ public  boolean swapParts(int first, int second){
 		StringArray.swapColumns(stateNotes, first, second);
 		Object2DArray.swapColumns(stateAnnotations, first, second);
 
-		return super.swapParts(first,second);
+		return super.swapParts(first,second, notify);
 
 	}
 	/*..........................................  CategoricalData  ..................................................*/
diff --git a/Source/mesquite/categ/lib/MProteinEmbedded.java b/Source/mesquite/categ/lib/MProteinEmbedded.java
index 4d276d90e..d3ebb5048 100644
--- a/Source/mesquite/categ/lib/MProteinEmbedded.java
+++ b/Source/mesquite/categ/lib/MProteinEmbedded.java
@@ -70,5 +70,22 @@ public long getAllStates() {  //
 		}
 		return s;
 	}
+	/*..........................................................*/
+	/** This readjust procedure can be called to readjust the size of storage of
+	states of a character for nodes. */
+	public MCharactersHistory adjustHistorySize(Tree tree, MCharactersHistory charStates) {
+		int numNodes = tree.getNumNodeSpaces();
+		MCharactersHistory soc =charStates;
+		if (charStates==null || ! (charStates.getClass() == MProteinHistory.class)) 
+			soc = new MProteinHistory(tree.getTaxa(), getNumChars(), numNodes); 
+		else if (numNodes!= charStates.getNumNodes() || charStates.getNumChars()!= getNumChars()) 
+			soc = new MProteinHistory(tree.getTaxa(), getNumChars(), numNodes);
+		else {
+			soc =charStates;
+		}
+		soc.setParentData(getParentData());
+		return soc;
+	}
+
 }
 
diff --git a/Source/mesquite/categ/lib/MolecularData.java b/Source/mesquite/categ/lib/MolecularData.java
index 6db2f6072..56815d62e 100644
--- a/Source/mesquite/categ/lib/MolecularData.java
+++ b/Source/mesquite/categ/lib/MolecularData.java
@@ -231,12 +231,12 @@ public boolean moveParts(int starting, int num, int justAfter){
 	}
 	/*-----------------------------------------------------------*/
 	/**Swaps characters first and second.*/
-	public boolean swapParts(int first, int second){
+	public boolean swapParts(int first, int second, boolean notify){
 		//swapping characters; deal with inversions
 		if (inversions != null){
 			MesquiteMessage.warnProgrammer("Swapping characters and strand inversions not yet fully supported");
 		}
-		return super.swapParts(first, second);
+		return super.swapParts(first, second, notify);
 	}
 	/*.................................................................................................................*/
 	protected CharacterState moveOne(int i, int distance, int it, CharacterState cs,  MesquiteBoolean dataChanged){
diff --git a/Source/mesquite/categ/lib/ProteinCharacterHistory.java b/Source/mesquite/categ/lib/ProteinCharacterHistory.java
index 657c0954d..904a955f9 100644
--- a/Source/mesquite/categ/lib/ProteinCharacterHistory.java
+++ b/Source/mesquite/categ/lib/ProteinCharacterHistory.java
@@ -135,7 +135,7 @@ public String toString (int node, String lineEnding) {
 			return s;
 		}
 		else
-			return ProteinState.toString(getState(node), null, 0, false);
+			return ProteinState.toString(getState(node), null, 0, false, true);
 	}
 	/*..........................................  ProteinCharacterHistory  ...................................................*/
 	/**returns string describing states at nodes. */
diff --git a/Source/mesquite/categ/lib/ProteinState.java b/Source/mesquite/categ/lib/ProteinState.java
index b2b54cc0d..78ea57a3e 100644
--- a/Source/mesquite/categ/lib/ProteinState.java
+++ b/Source/mesquite/categ/lib/ProteinState.java
@@ -125,7 +125,7 @@ public static String toString(long s, CategoricalData data, int ic, boolean useB
 		return toString(s, data, ic, useBraces, false);
 	}
 	/*..........................................ProteinState.....................................*/
-	/** converts passed long (treated as ProteinState) to string.  Uses character state names if available.*/
+	/** converts passed long (treated as ProteinState) to string.*/
 	public static String toString(long s, CategoricalData data, int ic, boolean useBraces, boolean useSymbols) {
 		if (s == impossible)
 			return "impossible";
@@ -152,7 +152,10 @@ else if (s == inapplicable){
 			if (isElement(s, e)) {
 				if (!first)
 					temp+=" ";
-				temp+=ProteinData.symbolsAsStrings[e];
+				if (useSymbols)  
+					temp+=ProteinData.symbolsAsStrings[e];
+				else
+					temp+=ProteinData.longNamesAsStrings[e];  //added Feb 2019
 				first=false;
 			}
 		}
@@ -161,7 +164,8 @@ else if (s == inapplicable){
 		if (useBraces)
 			temp+="}";
 		return temp;
-	}
+	}	
+
 	/*..........................................ProteinState.....................................*/
 	/**return the state set containing the state represented by the character (e.g., '0' to {0}) �*/
 	public long fromChar(char c) { 
diff --git a/Source/mesquite/charMatrices/BasicDataWindowMaker/BasicDataWindowMaker.java b/Source/mesquite/charMatrices/BasicDataWindowMaker/BasicDataWindowMaker.java
index a66f5941a..059baf346 100644
--- a/Source/mesquite/charMatrices/BasicDataWindowMaker/BasicDataWindowMaker.java
+++ b/Source/mesquite/charMatrices/BasicDataWindowMaker/BasicDataWindowMaker.java
@@ -302,6 +302,7 @@ class BasicDataWindow extends TableWindow implements MesquiteListener {
 	MesquiteBoolean useDiagonal = new MesquiteBoolean(false);
 	MesquiteBoolean allowAutosize;
 	boolean oldShowStates;
+	boolean oldReduceCellBorders;
 	boolean oldSuppress;
 	int oldColumnsWidths;
 	MesquiteMenuItemSpec linkedScrollingItem = null;
@@ -377,6 +378,7 @@ public BasicDataWindow(BasicDataWindowMaker ownerModule, CharacterData data) {
 		}
 
 		oldShowStates = table.showStates.getValue();
+		oldReduceCellBorders = table.reduceCellBorders.getValue();
 		oldColumnsWidths = table.getColumnWidthsUniform();
 		oldSuppress = table.suppressAutosize;
 		interleaved = new MesquiteBoolean(data.interleaved);
@@ -463,6 +465,8 @@ public BasicDataWindow(BasicDataWindowMaker ownerModule, CharacterData data) {
 		ownerModule.addCheckMenuItemToSubmenu(ownerModule.displayMenu, softnessSubmenu, "Lighten Missing", MesquiteModule.makeCommand("togglePaleMissing", this), table.paleMissing);
 		ownerModule.addCheckMenuItemToSubmenu(ownerModule.displayMenu, softnessSubmenu, "Lighten Excluded Characters", MesquiteModule.makeCommand("toggleShowPaleExcluded", this), showPaleExcluded);
 		
+		ownerModule.addCheckMenuItem(ownerModule.displayMenu,"Reduce Cell Borders", MesquiteModule.makeCommand("toggleReduceCellBorders", this), table.reduceCellBorders);
+
 		//CHANGES
 		ownerModule.addCheckMenuItem(ownerModule.displayMenu, "Show Changes Since Saved", MesquiteModule.makeCommand("toggleShowChanges", this), table.showChanges);
 		if (data instanceof CategoricalData && !(data instanceof DNAData) && !(data instanceof ProteinData))
@@ -912,6 +916,7 @@ public Snapshot getSnapshot(MesquiteFile file) {
 		temp.addLine("toggleShowChanges " + table.showChanges.toOffOnString());
 		temp.addLine("toggleSeparateLines " + table.statesSeparateLines.toOffOnString());
 		temp.addLine("toggleShowStates " + table.showStates.toOffOnString());
+		temp.addLine("toggleReduceCellBorders " + table.reduceCellBorders.toOffOnString());
 		temp.addLine("toggleAutoWCharNames " + table.autoWithCharNames.toOffOnString());
 		temp.addLine("toggleAutoTaxonNames " + table.autoRowNameWidth.toOffOnString());
 		temp.addLine("toggleShowDefaultCharNames " + table.showDefaultCharNames.toOffOnString());
@@ -1990,6 +1995,11 @@ else if (checker.compare(this.getClass(), "Sets whether or not states are to be
 			table.doAutosize = true;
 			table.repaintAll();
 		}
+		else if (checker.compare(this.getClass(), "Sets whether or not cell borders should be reduced", "[on or off]", commandName, "toggleReduceCellBorders")) {
+			table.reduceCellBorders.toggleValue(ParseUtil.getFirstToken(arguments, pos));
+			table.doAutosize = true;
+			table.repaintAll();
+		}
 		else if (checker.compare(this.getClass(), "Sets whether or not default character names are shown", "[on or off]", commandName, "toggleShowDefaultCharNames")) {
 			table.showDefaultCharNames.toggleValue(ParseUtil.getFirstToken(arguments, pos));
 			table.doAutosize = true;
@@ -2944,6 +2954,8 @@ class MatrixTable extends mesquite.lib.table.CMTable implements MesquiteDroppedF
 
 	MesquiteBoolean showStates;
 
+	MesquiteBoolean reduceCellBorders;
+
 	MesquiteBoolean showDefaultCharNames;
 
 	MesquiteBoolean autoWithCharNames;
@@ -3023,6 +3035,7 @@ public MatrixTable(BasicDataWindowMaker editorModule, BasicDataWindow window, Ch
 		this.data = data;
 		cellAnnotated = new CellAnnotation(data);
 		showStates = new MesquiteBoolean(true);
+		reduceCellBorders = new MesquiteBoolean(false);
 		showDefaultCharNames = new MesquiteBoolean(false);
 		autoWithCharNames = new MesquiteBoolean(!(data instanceof MolecularData));
 		showBirdsEyeView = new MesquiteBoolean(false);
@@ -3795,7 +3808,7 @@ public void drawMatrixCell(Graphics g, int x, int y, int w, int h, int column, i
 		if (data == null)
 			return;
 		boolean writeStates = !showBirdsEyeView.getValue() && showStates.getValue();
-		boolean leaveEdges = writeStates && !tight.getValue();
+		boolean leaveEdges = !reduceCellBorders.getValue() && writeStates && !tight.getValue();
 		drawMatrixCell(g, x, y, w, h, column, row, selected, writeStates, leaveEdges);
 
 	}
diff --git a/Source/mesquite/charMatrices/CompileProcessedMatrices/CompileProcessedMatrices.java b/Source/mesquite/charMatrices/CompileProcessedMatrices/CompileProcessedMatrices.java
index 41bdbe076..0c7439d9d 100644
--- a/Source/mesquite/charMatrices/CompileProcessedMatrices/CompileProcessedMatrices.java
+++ b/Source/mesquite/charMatrices/CompileProcessedMatrices/CompileProcessedMatrices.java
@@ -17,6 +17,7 @@
 import java.awt.FileDialog;
 import java.util.Vector;
 
+import mesquite.categ.lib.ProteinData;
 import mesquite.lib.*;
 import mesquite.lib.characters.CharacterData;
 import mesquite.lib.duties.*;
@@ -77,7 +78,10 @@ void checkTaxonList(CharacterData data, String saveFile){
 	void writeMatrixToFile(String file, CharacterData data, String matrixName){
 		MesquiteFile.appendFileContents(file, "BEGIN CHARACTERS;" + StringUtil.lineEnding() + "\tTITLE " + ParseUtil.tokenize(matrixName) + ";" + StringUtil.lineEnding() , true);
 		MesquiteFile.appendFileContents(file, "\tDIMENSIONS NCHAR= " + data.getNumChars() + " ;" + StringUtil.lineEnding() , true);
-		MesquiteFile.appendFileContents(file, "\tFORMAT DATATYPE = DNA GAP = - MISSING = ?;" + StringUtil.lineEnding() + "\tMATRIX" + StringUtil.lineEnding() , true);
+		if (data instanceof ProteinData)
+			MesquiteFile.appendFileContents(file, "\tFORMAT DATATYPE = PROTEIN GAP = - MISSING = ?;" + StringUtil.lineEnding() + "\tMATRIX" + StringUtil.lineEnding() , true);
+		else
+			MesquiteFile.appendFileContents(file, "\tFORMAT DATATYPE = DNA GAP = - MISSING = ?;" + StringUtil.lineEnding() + "\tMATRIX" + StringUtil.lineEnding() , true);
 		for (int it = 0; it < data.getNumTaxa(); it++){
 			MesquiteFile.appendFileContents(file, "\t" + ParseUtil.tokenize(data.getTaxa().getTaxonName(it)) + "\t" , true);
 			StringBuffer description = new StringBuffer();
@@ -95,7 +99,7 @@ public boolean processFile(MesquiteFile file){
 
 		if (saveFile == null || okToInteractWithUser(CAN_PROCEED_ANYWAY, "Asking for file to save")){ //need to check if can proceed
 
-			MesquiteFileDialog fdlg= new MesquiteFileDialog(containerOfModule(), "Output File for Matrices(s)", FileDialog.SAVE);
+			MesquiteFileDialog fdlg= new MesquiteFileDialog(containerOfModule(), "Output File for Compiled Matrices(s)", FileDialog.SAVE);
 			fdlg.setBackground(ColorTheme.getInterfaceBackground());
 			fdlg.setVisible(true);
 			String fileName=fdlg.getFile();
diff --git a/Source/mesquite/charMatrices/CondensedPatternMatrix/CondensedPatternMatrix.java b/Source/mesquite/charMatrices/CondensedPatternMatrix/CondensedPatternMatrix.java
index 77778f09f..c6480020d 100644
--- a/Source/mesquite/charMatrices/CondensedPatternMatrix/CondensedPatternMatrix.java
+++ b/Source/mesquite/charMatrices/CondensedPatternMatrix/CondensedPatternMatrix.java
@@ -125,8 +125,8 @@ private MCharactersDistribution condense(MCharactersDistribution mData){
 						}
 					}
 					if (bestCharacter>=0 && ic<newNumChars){
-						weightSet.swapParts(ic+1, bestCharacter);
-						condensedData.swapParts(ic+1, bestCharacter);
+						weightSet.swapParts(ic+1, bestCharacter, true);
+						condensedData.swapParts(ic+1, bestCharacter, true);
 					}
 				}
 				condensedData.setCurrentSpecsSet(weightSet, CharWeightSet.class); 
diff --git a/Source/mesquite/charMatrices/ManageCharacters/ManageCharacters.java b/Source/mesquite/charMatrices/ManageCharacters/ManageCharacters.java
index 3b14e0241..ba5ceb0ed 100644
--- a/Source/mesquite/charMatrices/ManageCharacters/ManageCharacters.java
+++ b/Source/mesquite/charMatrices/ManageCharacters/ManageCharacters.java
@@ -94,6 +94,8 @@ public MesquiteModule showElement(FileElement e){
 			CharacterData t = (CharacterData)e;
 			return showMatrixEditor(t);
 		}
+		if (e == getProject().datas)
+			return showListOfCharacterMatrices(null);
 		return null;
 	}
 	/*.................................................................................................................*/
@@ -951,29 +953,7 @@ else if (checker.compare(this.getClass(), "Creates a new character data matrix f
 			}
 		}
 		else if (checker.compare(this.getClass(), "Shows list of data matrices", null, commandName, "showDatasList")) {
-			String concatMessage = "To concatenate matrices, select their rows in the List of Character Matrices window, and choose List>Utilities>Concatenate Selected Matrices.";
-			//Check to see if already has lister for this
-			for (int i = 0; i<getNumberOfEmployees(); i++) {
-				Object e=getEmployeeVector().elementAt(i);
-				if (e instanceof ManagerAssistant)
-					if (((ManagerAssistant)e).getName().equals("Character Matrices List")) {
-						((ManagerAssistant)e).getModuleWindow().setVisible(true);
-						if ("concat".equalsIgnoreCase(arguments))
-							discreetAlert(concatMessage);
-						return e;
-					}
-			}
-			ManagerAssistant lister= (ManagerAssistant)hireNamedEmployee(ManagerAssistant.class, StringUtil.tokenize("Character Matrices List"));
-			if (lister==null){
-				alert("Sorry, no module was found to list the character data matrices");
-				return null;
-			}
-			lister.showListWindow(null);
-			if (!MesquiteThread.isScripting() && lister.getModuleWindow()!=null)
-				lister.getModuleWindow().setVisible(true);
-			if ("concat".equalsIgnoreCase(arguments))
-				discreetAlert(concatMessage);
-			return lister;
+			return showListOfCharacterMatrices(arguments);
 		}
 		else if (checker.compare(this.getClass(), "Deletes matrices from the project", null, commandName, "deleteMatrices")) {
 			Listable[] chosen = ListDialog.queryListMultiple(containerOfModule(), "Select Matrices to Delete", "Select one or more character matrices to be deleted", (String)null, "Delete", false, getProject().getCharacterMatrices(), (boolean[])null);
@@ -1098,6 +1078,32 @@ else if (checker.compare(this.getClass(), "Closes all list of characters windows
 			return  super.doCommand(commandName, arguments, checker);
 		return null;
 	}
+	
+	public MesquiteModule showListOfCharacterMatrices(String arguments){
+		String concatMessage = "To concatenate matrices, select their rows in the List of Character Matrices window, and choose List>Utilities>Concatenate Selected Matrices.";
+		//Check to see if already has lister for this
+		for (int i = 0; i<getNumberOfEmployees(); i++) {
+			Object e=getEmployeeVector().elementAt(i);
+			if (e instanceof ManagerAssistant)
+				if (((ManagerAssistant)e).getName().equals("Character Matrices List")) {
+					((ManagerAssistant)e).getModuleWindow().setVisible(true);
+					if ("concat".equalsIgnoreCase(arguments))
+						discreetAlert(concatMessage);
+					return (MesquiteModule)e;
+				}
+		}
+		ManagerAssistant lister= (ManagerAssistant)hireNamedEmployee(ManagerAssistant.class, StringUtil.tokenize("Character Matrices List"));
+		if (lister==null){
+			alert("Sorry, no module was found to list the character data matrices");
+			return null;
+		}
+		lister.showListWindow(null);
+		if (!MesquiteThread.isScripting() && lister.getModuleWindow()!=null)
+			lister.getModuleWindow().setVisible(true);
+		if ("concat".equalsIgnoreCase(arguments))
+			discreetAlert(concatMessage);
+		return lister;
+	}
 	/*.................................................................................................................*/
 	/** returns number of data sets of given reference string (ref. number, name, number) from the project */
 	public int  getNumberCharMatricesWithUniqueID(String uniqueID) {  //ManageCharacters Only
diff --git a/Source/mesquite/charMatrices/NumMatricesWithDataForTaxon/NumMatricesWithDataForTaxon.java b/Source/mesquite/charMatrices/NumMatricesWithDataForTaxon/NumMatricesWithDataForTaxon.java
new file mode 100644
index 000000000..4c257f28d
--- /dev/null
+++ b/Source/mesquite/charMatrices/NumMatricesWithDataForTaxon/NumMatricesWithDataForTaxon.java
@@ -0,0 +1,103 @@
+/* Mesquite source code.  Copyright 1997 and onward, W. Maddison and D. Maddison. 
+
+
+Disclaimer:  The Mesquite source code is lengthy and we are few.  There are no doubt inefficiencies and goofs in this code. 
+The commenting leaves much to be desired. Please approach this source code with the spirit of helping out.
+Perhaps with your help we can be more than a few, and make Mesquite better.
+
+Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.
+Mesquite's web site is http://mesquiteproject.org
+
+This source code and its compiled class files are free and modifiable under the terms of 
+GNU Lesser General Public License.  (http://www.gnu.org/copyleft/lesser.html)
+*/
+
+package mesquite.charMatrices.NumMatricesWithDataForTaxon;
+
+import mesquite.lib.MesquiteNumber;
+import mesquite.lib.MesquiteString;
+import mesquite.lib.Notification;
+import mesquite.lib.Taxa;
+import mesquite.lib.Taxon;
+import mesquite.lib.characters.CharacterData;
+import mesquite.lib.duties.NumberForTaxon;
+
+public class NumMatricesWithDataForTaxon extends NumberForTaxon {
+	/*.................................................................................................................*/
+	public boolean startJob(String arguments, Object condition, boolean hiredByName) {
+		getProject().addListener(this);
+		return true;
+	}
+	public void endJob(){
+		super.endJob();
+		getProject().removeListener(this);
+	}
+	/* ---------------------------------------------------------*/
+	/** passes which object changed, along with optional Notification object with details (e.g., code number (type of change) and integers (e.g. which character))*/
+	public void changed(Object caller, Object obj, Notification notification){
+		outputInvalid();
+		parametersChanged();
+	}
+	/*.................................................................................................................*/
+	/** returns whether this module is requesting to appear as a primary choice */
+	public boolean requestPrimaryChoice(){
+		return false;  
+	}
+
+	/** Called to provoke any necessary initialization.  This helps prevent the module's initialization queries to the user from
+	   	happening at inopportune times (e.g., while a long chart calculation is in mid-progress)*/
+	public void initialize(Taxa taxa){
+	}
+
+	/*.................................................................................................................*/
+	/** returns the version number at which this module was first released.  If 0, then no version number is claimed.  If a POSITIVE integer
+	 * then the number refers to the Mesquite version.  This should be used only by modules part of the core release of Mesquite.
+	 * If a NEGATIVE integer, then the number refers to the local version of the package, e.g. a third party package*/
+	public int getVersionOfFirstRelease(){
+		return 361;  
+	}
+	/*.................................................................................................................*/
+	public String getName() {
+		return "Number of Matrices with Data for Taxon";  
+	}
+
+	/*.................................................................................................................*/
+	public boolean isPrerelease() {
+		return false;
+	}
+	/*.................................................................................................................*/
+	public boolean isSubstantive() {
+		return true;
+	}
+
+	/*.................................................................................................................*/
+
+	/** returns an explanation of what the module does.*/
+	public String getExplanation() {
+		return "Reports for how many matrices the taxon has data." ;
+	}
+	public void calculateNumber(Taxon taxon, MesquiteNumber result, MesquiteString resultString){
+		if (result==null)
+			return;
+		result.setToUnassigned();
+		Taxa taxa = taxon.getTaxa();
+		int it = taxon.getIndex();
+		clearResultAndLastResult(result);
+		int count = 0;
+		for (int im = 0; im < getProject().getNumberCharMatrices(taxa); im++){
+			CharacterData data = getProject().getCharacterMatrix(taxa, im);
+			if (data.hasDataForTaxon(it)){
+				count++;
+			}
+		}
+		result.setValue(count);
+
+		if (resultString!=null){
+				resultString.setValue(result.toString());
+		}
+		saveLastResult(result);
+		saveLastResultString(resultString);
+	}
+}
+
+
diff --git a/Source/mesquite/charMatrices/NumSelTaxaWithDataInMatrix/NumSelTaxaWithDataInMatrix.java b/Source/mesquite/charMatrices/NumSelTaxaWithDataInMatrix/NumSelTaxaWithDataInMatrix.java
new file mode 100644
index 000000000..afb5d9f4c
--- /dev/null
+++ b/Source/mesquite/charMatrices/NumSelTaxaWithDataInMatrix/NumSelTaxaWithDataInMatrix.java
@@ -0,0 +1,105 @@
+/* Mesquite source code.  Copyright 1997 and onward, W. Maddison and D. Maddison. 
+
+
+Disclaimer:  The Mesquite source code is lengthy and we are few.  There are no doubt inefficiencies and goofs in this code. 
+The commenting leaves much to be desired. Please approach this source code with the spirit of helping out.
+Perhaps with your help we can be more than a few, and make Mesquite better.
+
+Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.
+Mesquite's web site is http://mesquiteproject.org
+
+This source code and its compiled class files are free and modifiable under the terms of 
+GNU Lesser General Public License.  (http://www.gnu.org/copyleft/lesser.html)
+*/
+
+package mesquite.charMatrices.NumSelTaxaWithDataInMatrix;
+
+
+
+import mesquite.lib.*;
+import mesquite.lib.characters.*;
+import mesquite.lib.duties.*;
+
+public class NumSelTaxaWithDataInMatrix extends NumberForMatrix {
+
+	public boolean startJob(String arguments, Object condition, boolean hiredByName) {
+		return true;
+	} 
+
+	public void endJob(){
+		for (int i = 0; i< getProject().getNumberTaxas(); i++)
+			getProject().getTaxa(i).removeListener(this);
+		super.endJob();
+	}
+	/*.................................................................................................................*/
+	/** returns the version number at which this module was first released.  If 0, then no version number is claimed.  If a POSITIVE integer
+	 * then the number refers to the Mesquite version.  This should be used only by modules part of the core release of Mesquite.
+	 * If a NEGATIVE integer, then the number refers to the local version of the package, e.g. a third party package*/
+	public int getVersionOfFirstRelease(){
+		return 361;  
+	}
+	/** Called to provoke any necessary initialization.  This helps prevent the module's initialization queries to the user from happening at inopportune times (e.p., while a long chart calculation is in mid-progress*/
+	public void initialize(MCharactersDistribution data) {
+	} 
+	/* ---------------------------------------------------------*/
+	/** passes which object changed, along with optional Notification object with details (e.g., code number (type of change) and integers (e.g. which character))*/
+	public void changed(Object caller, Object obj, Notification notification){
+		outputInvalid();
+		parametersChanged();
+	}
+
+	public void calculateNumber(MCharactersDistribution data, MesquiteNumber result, MesquiteString resultString) {
+		if (result == null || data == null)
+			return;
+		clearResultAndLastResult(result);
+		int count = 0;
+		Taxa taxa = data.getTaxa();
+		taxa.addListener(this); //this doesn't add if it's already there
+		boolean anySelected = taxa.anySelected();
+		for (int it = 0; it<data.getNumTaxa(); it++){
+			if ((!anySelected || taxa.getSelected(it)) && hasData(data, it))
+				count++;
+		}
+
+
+		if (count>0) {
+			result.setValue(count); 
+		}  else
+			result.setValue(0.0); 
+
+		if (resultString!=null) {
+			resultString.setValue("Number of selected taxa with data: " + result.toString());
+		}
+		saveLastResult(result);
+		saveLastResultString(resultString);
+	} 
+	boolean hasData(MCharactersDistribution data, int it){
+		CharacterState cs = null;
+		try {
+			for (int ic=0; ic<data.getNumChars(); ic++) {
+				cs = data.getCharacterState(cs, ic, it);
+				if (cs == null)
+					return false;
+				if (!cs.isInapplicable() && !cs.isUnassigned()) 
+					return true;
+
+			}
+		}
+		catch (NullPointerException e){
+		}
+		return false;
+	}
+
+	public boolean isPrerelease (){
+		return false;
+	}
+
+	public String getName() {
+		return "Number of Selected Taxa with Data in Matrix";
+	} 
+
+	public String getExplanation(){
+		return "Counts the number of taxa, among those selected, with data (not ? and not gaps) the matrix.";
+	} 
+
+} 
diff --git a/Source/mesquite/charMatrices/SortChar/SortChar.java b/Source/mesquite/charMatrices/SortChar/SortChar.java
index 4808b0fc4..2b50f5934 100644
--- a/Source/mesquite/charMatrices/SortChar/SortChar.java
+++ b/Source/mesquite/charMatrices/SortChar/SortChar.java
@@ -88,7 +88,7 @@ void swapParts(CharacterData data, int first, int second, String[] text){
   		String temp = text[first];
   		text[first] = text[second];
   		text[second] = temp;
-		data.swapParts(first, second); 
+		data.swapParts(first, second, true); 
 		data.swapInLinked(first, second, false); 
 	}
 	MesquiteInteger pos = new MesquiteInteger();
@@ -144,7 +144,7 @@ public Object doCommand(String commandName, String arguments, CommandChecker che
 					for (int i=1; i<data.getNumChars(); i++) {
 						if (i % 10 == 0) CommandRecord.tick("Sorting from character " + i);
 						for (int j= i-1; j>=0 && compare(gT, data.getCharacterName(j), data.getCharacterName(j+1)); j--) {
-							data.swapParts(j, j+1);
+							data.swapParts(j, j+1, false);
 							data.swapInLinked(j, j+1, false);
 						}
 					}
diff --git a/Source/mesquite/charMatrices/SortTaxa/SortTaxa.java b/Source/mesquite/charMatrices/SortTaxa/SortTaxa.java
index 69ab1984a..4fef4a9a8 100644
--- a/Source/mesquite/charMatrices/SortTaxa/SortTaxa.java
+++ b/Source/mesquite/charMatrices/SortTaxa/SortTaxa.java
@@ -90,7 +90,7 @@ void swapParts(Taxa taxa, int first, int second, String[] text){
   		String temp = text[first];
   		text[first] = text[second];
   		text[second] = temp;
-		taxa.swapParts(first, second); 
+		taxa.swapParts(first, second, true); 
 	}
 	MesquiteInteger pos = new MesquiteInteger();
 	 
diff --git a/Source/mesquite/cont/lib/ContinuousData.java b/Source/mesquite/cont/lib/ContinuousData.java
index eb5703576..9290eba46 100644
--- a/Source/mesquite/cont/lib/ContinuousData.java
+++ b/Source/mesquite/cont/lib/ContinuousData.java
@@ -425,7 +425,7 @@ else if (starting>numChars)
 	}
 	/*..........................................ContinuousData................*/
 	/**swaps characters first and second.*/
-	public boolean swapParts(int first, int second){
+	public boolean swapParts(int first, int second, boolean notify){
 		if (first<0 || first >= numChars)
 			return false;
 		if (second<0 || second >= numChars)
@@ -434,7 +434,7 @@ public boolean swapParts(int first, int second){
 			Double2DArray oldMatrix = ((Double2DArray)matrices.elementAt(item));
 			Double2DArray.swapColumns(oldMatrix.getMatrix(), first, second);
 		}
-		return super.swapParts(first, second);
+		return super.swapParts(first, second, notify);
 	}
 	/*..........................................ContinuousData................*/
 	/**moves num characters from position "first" to just after position "justAfter"; returns true iff successful.*/
diff --git a/Source/mesquite/distance/ExportTaxaDistancesByGroup/ExportTaxaDistancesByGroup.java b/Source/mesquite/distance/ExportTaxaDistancesByGroup/ExportTaxaDistancesByGroup.java
new file mode 100644
index 000000000..876a9d22d
--- /dev/null
+++ b/Source/mesquite/distance/ExportTaxaDistancesByGroup/ExportTaxaDistancesByGroup.java
@@ -0,0 +1,243 @@
+/* Mesquite source code.  Copyright 1997 and onward, W. Maddison and D. Maddison. 
+
+
+Disclaimer:  The Mesquite source code is lengthy and we are few.  There are no doubt inefficiencies and goofs in this code. 
+The commenting leaves much to be desired. Please approach this source code with the spirit of helping out.
+Perhaps with your help we can be more than a few, and make Mesquite better.
+
+Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.
+Mesquite's web site is http://mesquiteproject.org
+
+This source code and its compiled class files are free and modifiable under the terms of 
+GNU Lesser General Public License.  (http://www.gnu.org/copyleft/lesser.html)
+ */
+package mesquite.distance.ExportTaxaDistancesByGroup;
+
+
+import java.util.*;
+import java.awt.*;
+
+import mesquite.lib.*;
+import mesquite.lib.duties.*;
+import mesquite.distance.lib.*;
+
+
+
+public class ExportTaxaDistancesByGroup extends FileInterpreterI {
+	TaxaDistanceSource distanceTask;
+	Taxa currentTaxa = null;
+	boolean suspend = false;
+
+	/*.................................................................................................................*/
+	public boolean startJob(String arguments, Object condition, boolean hiredByName) {
+		return true;  //make this depend on taxa reader being found?)
+	}
+
+	public boolean isPrerelease(){
+		return true;
+	}
+	public boolean loadModule(){
+		return false;
+	}
+	public boolean isSubstantive(){
+		return true;
+	}
+	/*.................................................................................................................*/
+	public String preferredDataFileExtension() {
+		return "txt";
+	}
+	/*.................................................................................................................*/
+	public boolean canExportEver() {  
+		return true;  //
+	}
+	/*.................................................................................................................*/
+	public boolean canExportProject(MesquiteProject project) {  
+		return true;
+	}
+
+	/*.................................................................................................................*/
+	public boolean canExportData(Class dataClass) {  
+		return false;
+	}
+	/*.................................................................................................................*/
+	public boolean canImport() {  
+		return false;
+	}
+
+	/*.................................................................................................................*/
+	public void readFile(MesquiteProject mf, MesquiteFile file, String arguments) {
+	}
+	/*.................................................................................................................*/
+	/** returns the version number at which this module was first released.  If 0, then no version number is claimed.  If a POSITIVE integer
+	 * then the number refers to the Mesquite version.  This should be used only by modules part of the core release of Mesquite.
+	 * If a NEGATIVE integer, then the number refers to the local version of the package, e.g. a third party package*/
+	public int getVersionOfFirstRelease(){
+		return NEXTRELEASE;  
+	}
+
+
+	/* ============================  exporting ============================*/
+	/*.................................................................................................................*/
+	String fileName = "distances.txt";
+	String addendum = "";
+	/*
+	public boolean getExportOptions(Taxa taxa){
+		MesquiteInteger buttonPressed = new MesquiteInteger(1);
+		ExporterDialog exportDialog = new ExporterDialog(this,containerOfModule(), "Export distance matrix", buttonPressed);
+		exportDialog.setSuppressLineEndQuery(true);
+		exportDialog.setDefaultButton(null);
+		exportDialog.addLargeOrSmallTextLabel("Distances are to be exported from:\n\n" + distanceTask.getNameAndParameters());
+/ *		Checkbox itCheckBox = exportDialog.addCheckBox("Include Taxa Block", includeTaxaBlock);
+		exportDialog.addLabel("Addendum: ");
+
+		addendum = "";
+
+		TextArea fsText =exportDialog.addTextAreaSmallFont(addendum,16);
+	 * /
+		exportDialog.completeAndShowDialog();
+
+		boolean ok = (exportDialog.query()==0);
+
+
+		exportDialog.dispose();
+		return ok;
+	}	
+	/*.................................................................................................................*/
+	/** Called to provoke any necessary initialization.  This helps prevent the module's initialization queries to the user from
+   	happening at inopportune times (e.g., while a long chart calculation is in mid-progress)*/
+	public void initialize(Taxa taxa){
+		setPreferredTaxa(taxa);
+		distanceTask = (TaxaDistanceSource)hireEmployee(TaxaDistanceSource.class, "Source of Distances among Taxa");
+		if (distanceTask == null)
+			return;
+	}
+	public void endJob(){
+		if (currentTaxa!=null)
+			currentTaxa.removeListener(this);
+		storePreferences();
+		super.endJob();
+	}
+	/*.................................................................................................................*/
+	/** passes which object changed*/
+	public void disposing(Object obj){
+		if (obj == currentTaxa) {
+			currentTaxa = null;
+		}
+	}
+
+	/*.................................................................................................................*/
+
+	public void setPreferredTaxa(Taxa taxa){
+		if (taxa !=currentTaxa) {
+			if (currentTaxa!=null)
+				currentTaxa.removeListener(this);
+			currentTaxa = taxa;
+			currentTaxa.addListener(this);
+		}
+
+	}
+
+	/*.................................................................................................................*/
+	public boolean exportFile(MesquiteFile file, String arguments) { //if file is null, consider whole project open to export
+		Arguments args = new Arguments(new Parser(arguments), true);
+
+		Taxa taxa = 	 getProject().chooseTaxa(getModuleWindow(), "Choose taxa block"); 
+		if (taxa==null) 
+			return false;
+
+		if (distanceTask==null || taxa!=currentTaxa) {
+			initialize(taxa);
+			if (distanceTask==null)
+				return false;
+			distanceTask.initialize(currentTaxa);
+		}
+
+
+		MesquiteString dir = new MesquiteString();
+		MesquiteString fn = new MesquiteString();
+		String suggested = fileName;
+		if (file !=null) {
+			suggested = file.getFileName();
+			if (StringUtil.getLastItem(suggested, ".").equalsIgnoreCase("nex")) {
+				suggested = StringUtil.getAllButLastItem(suggested, ".") +".distances.txt";
+			}
+			else	if (StringUtil.getLastItem(suggested, ".").equalsIgnoreCase("nxs")) {
+				suggested = StringUtil.getAllButLastItem(suggested, ".") +".distances.txt";
+			}else
+				suggested = suggested +".distances.txt";
+		}
+
+		MesquiteFile f;
+		/*if (!usePrevious){
+			if (!getExportOptions(null)) {
+				distanceTask=null;
+				return false;
+			}
+		}
+		 */
+		if (!distanceTask.getDistanceOptions()) {
+			fireEmployee(distanceTask);
+			distanceTask=null;
+			return false;
+		}
+		TaxaDistance distances = distanceTask.getTaxaDistance(taxa);
+		if (distances == null){
+			return false;
+		}
+		TaxaPartition partitions = (TaxaPartition)taxa.getCurrentSpecsSet(TaxaPartition.class);
+
+		String path = getPathForExport(arguments, suggested, dir, fn);
+		if (path != null) {
+			f = MesquiteFile.newFile(dir.getValue(), fn.getValue());
+			if (f !=null){
+				f.openWriting(true);
+				StringBuffer line = new StringBuffer(1000);
+				for (int it = 0; it<taxa.getNumTaxa(); it++){
+					TaxaGroup groupOfTaxon = (TaxaGroup)partitions.getProperty(it);
+					if (groupOfTaxon!=null) {
+						for (int it2 = 0; it2<taxa.getNumTaxa(); it2++){
+							TaxaGroup comparisonGroup = (TaxaGroup)partitions.getProperty(it2);
+							if (groupOfTaxon.equals(comparisonGroup)) {
+								line.setLength(0);
+								line.append(taxa.getTaxonName(it) +"\t"+groupOfTaxon.getName()+"-"+groupOfTaxon.getName()+"\twithin\t");
+								line.append(MesquiteDouble.toString(distances.getDistance(it, it2)));							
+								f.writeLine(line.toString());
+							}
+						}
+						for (int it2 = 0; it2<taxa.getNumTaxa(); it2++){
+							TaxaGroup comparisonGroup = (TaxaGroup)partitions.getProperty(it2);
+							if (!groupOfTaxon.equals(comparisonGroup) && comparisonGroup!=null) {
+								line.setLength(0);
+								line.append(taxa.getTaxonName(it) +"\t"+groupOfTaxon.getName()+"-"+comparisonGroup.getName()+"\tbetween\t");
+								line.append(MesquiteDouble.toString(distances.getDistance(it, it2)));							
+								f.writeLine(line.toString());
+							}
+						}
+					}
+				}
+				f.closeWriting();
+				fireEmployee(distanceTask);
+				distanceTask=null;
+				return true;
+			}
+		}
+		fireEmployee(distanceTask);
+		distanceTask=null;
+		return false;
+	}
+
+	/*.................................................................................................................*/
+	public String getName() {
+		return "Export Distances Within and Between Groups";
+	}
+	/*.................................................................................................................*/
+
+	/** returns an explanation of what the module does.*/
+	public String getExplanation() {
+		String s =  "Exports a text file with distances within groups distinguished from those between groups." ;
+		return s;
+	}
+	/*.................................................................................................................*/
+
+}
+
diff --git a/Source/mesquite/dmanager/RandomizeTaxonOrder/RandomizeTaxonOrder.java b/Source/mesquite/dmanager/RandomizeTaxonOrder/RandomizeTaxonOrder.java
index 49181caea..d047502b5 100644
--- a/Source/mesquite/dmanager/RandomizeTaxonOrder/RandomizeTaxonOrder.java
+++ b/Source/mesquite/dmanager/RandomizeTaxonOrder/RandomizeTaxonOrder.java
@@ -42,7 +42,7 @@ void swapParts(Associable assoc, int first, int second, int[] nums){
   		int temp = nums[first];
   		nums[first] = nums[second];
   		nums[second] = temp;
-		assoc.swapParts(first, second); 
+		assoc.swapParts(first, second, true); 
 	}
 	/** Called to operate on the taxa in the block.  Returns true if taxa altered*/
 	public  boolean operateOnTaxa(Taxa taxa){
diff --git a/Source/mesquite/dmanager/TaxonNameFromSampleNamesFile/TaxonNameFromSampleNamesFile.java b/Source/mesquite/dmanager/TaxonNameFromSampleNamesFile/TaxonNameFromSampleNamesFile.java
index c304fadbe..4295ffbdd 100644
--- a/Source/mesquite/dmanager/TaxonNameFromSampleNamesFile/TaxonNameFromSampleNamesFile.java
+++ b/Source/mesquite/dmanager/TaxonNameFromSampleNamesFile/TaxonNameFromSampleNamesFile.java
@@ -33,6 +33,8 @@ public class TaxonNameFromSampleNamesFile extends TaxonNameAlterer implements Ac
 	MesquiteBoolean matchCurrentTaxonName = new MesquiteBoolean(true);
 	MesquiteBoolean changeColor = new MesquiteBoolean(true);
 	String[] nameCategories = new String[]{"<choose column>"};
+	
+	//TODO: note that the sample code in the names file CANNOT contain "/" 
 
 	public boolean startJob(String arguments, Object condition, boolean hiredByName) {
 		loadPreferences();
@@ -273,6 +275,8 @@ public  String getSeqNamesFromTabDelimitedFile(MesquiteString sampleCode, String
 			MesquiteMessage.warnUser("Taxon \"" + taxonName + "\" has no target string to match.");
 			return null;
 		}
+		if (sampleCodeString.contains("/"))  // if there is more than one item, then take only the first one.
+			sampleCodeString = StringUtil.getFirstItem(sampleCodeString, "/");
 		for (int row = 0; row<sampleCodeList.length; row++){
 			if (chosenNameCategory< sampleCodeList[row].length){
 				String code = sampleCodeList[row][0];
diff --git a/Source/mesquite/dmanager/lib/ProcessDataFilesLib.java b/Source/mesquite/dmanager/lib/ProcessDataFilesLib.java
index 7278242dc..82f0c8aa9 100644
--- a/Source/mesquite/dmanager/lib/ProcessDataFilesLib.java
+++ b/Source/mesquite/dmanager/lib/ProcessDataFilesLib.java
@@ -38,7 +38,7 @@ public class ProcessDataFilesLib extends GeneralFileMaker {
 
 	protected String script = null;
 	protected boolean incorporateScript = false;
-
+	private MesquiteBoolean rRAN = new MesquiteBoolean();
 	/*.................................................................................................................*/
 	public boolean startJob(String arguments, Object condition, boolean hiredByName){
 		loadPreferences();
@@ -48,12 +48,22 @@ public boolean startJob(String arguments, Object condition, boolean hiredByName)
 	public void processSingleXMLPreference (String tag, String content) {
 		if ("script".equalsIgnoreCase(tag))
 			script = StringUtil.cleanXMLEscapeCharacters(content);
-
+		else if ("importerString".equalsIgnoreCase(tag))
+			importerString = StringUtil.cleanXMLEscapeCharacters(content);
+		else if ("fileExtension".equalsIgnoreCase(tag))
+			fileExtension = StringUtil.cleanXMLEscapeCharacters(content);
+		else if ("autoNEXUSSave".equalsIgnoreCase(tag)){
+				rRAN.setValue(content);
+				autoNEXUSSave = rRAN.getValue();
+		}
 	}
 	/*.................................................................................................................*/
 	public String preparePreferencesForXML () {
 		StringBuffer buffer = new StringBuffer(60);	
 		StringUtil.appendXMLTag(buffer, 2, "script", script);  
+		StringUtil.appendXMLTag(buffer, 2, "importerString", importerString);  
+		StringUtil.appendXMLTag(buffer, 2, "fileExtension", fileExtension);  
+		StringUtil.appendXMLTag(buffer, 2, "autoNEXUSSave", autoNEXUSSave);  
 		return buffer.toString();
 	}
 	/*.................................................................................................................*/
@@ -197,6 +207,34 @@ protected String getSavedFilesDirectoryPath(MesquiteFile fileToRead) {
 		return fileToRead.getDirectoryName() + "savedFiles" + MesquiteFile.fileSeparator;
 	}
 	/*.................................................................................................................*/
+	protected boolean beforeProcessFiles() {
+		if (fileProcessors != null){
+			boolean success = true;
+			for (int i= 0; i< fileProcessors.size() && success; i++){
+				FileProcessor alterer = (FileProcessor)fileProcessors.elementAt(i);
+				success = alterer.beforeProcessingSeriesOfFiles();
+				if (!success)
+					logln("Sorry,  " + alterer.getNameAndParameters() + " did not succeed.");
+			}
+			return success;
+		}
+		return true;
+	}
+	/*.................................................................................................................*/
+	protected boolean afterProcessFiles() {
+		if (fileProcessors != null){
+			boolean success = true;
+			for (int i= 0; i< fileProcessors.size() && success; i++){
+				FileProcessor alterer = (FileProcessor)fileProcessors.elementAt(i);
+				success = alterer.afterProcessingSeriesOfFiles();
+				if (!success)
+					logln("Sorry,  " + alterer.getNameAndParameters() + " did not succeed.");
+			}
+			return success;
+		}
+		return true;
+	}
+	/*.................................................................................................................*/
 	protected boolean processFile(MesquiteFile fileToRead, StringBuffer results, MesquiteBoolean requestToSequester) {
 		logln("Processing file " + fileToRead.getName() + " in " + fileToRead.getDirectoryName() + "...");
 		incrementMenuResetSuppression();
@@ -285,6 +323,12 @@ protected void adjustFile(MesquiteFile fileToWrite){
 	static boolean autoNEXUSSave = true;
 	static String fileExtension = "";
 	/*.................................................................................................................*/
+	public void addOptions (ExtensibleDialog dialog) {
+	}
+	/*.................................................................................................................*/
+	public void processOptions () {
+	}
+	/*.................................................................................................................*/
 	public boolean queryOptions() {
 		MesquiteInteger buttonPressed = new MesquiteInteger(1);
 		ExtensibleDialog dialog = new ExtensibleDialog(containerOfModule(), "Process file options",buttonPressed);  //MesquiteTrunk.mesquiteTrunk.containerOfModule()
@@ -292,14 +336,18 @@ public boolean queryOptions() {
 		dialog.appendToHelpString("This dialog box provides various file-handling options for the files processed. ");
 		dialog.appendToHelpString("You can restrict which files are processed by specifying an extension, and you can ask for all the files to be resaved as NEXUS files. ");
 		dialog.appendToHelpString("Subsequent dialog boxes will provide additional processing options. ");
-		SingleLineTextField extension = dialog.addTextField ("Process only files with this extension (e.g. .nex, .fas): ", "", 5);
+		
+		SingleLineTextField extension = dialog.addTextField ("Process only files with this extension (e.g. .nex, .fas): ", fileExtension, 5);
 		Checkbox autoSave = dialog.addCheckBox("Resave all files as NEXUS", autoNEXUSSave);
+		addOptions(dialog);
 
 		dialog.completeAndShowDialog(true);
 		if (buttonPressed.getValue()==0)  {
 			autoNEXUSSave=autoSave.getState();
 			fileExtension = extension.getText();
-			//storePreferences();
+			
+			processOptions();
+			storePreferences();
 
 		}
 		dialog.dispose();
@@ -335,6 +383,7 @@ protected  void processDirectory(String directoryPath){
 					logln(StringUtil.getDateTime(dnow));
 					header += StringUtil.getDateTime(dnow) + StringUtil.lineEnding() + StringUtil.lineEnding();
 					MesquiteFile.putFileContents(writingFile.getDirectoryName() + "ProcessingResults.txt", header, true);
+					beforeProcessFiles();
 					for (int i=0; i<files.length; i++) {
 						progIndicator.setCurrentValue(i);
 						requestToSequester.setValue(false);
@@ -377,6 +426,7 @@ protected  void processDirectory(String directoryPath){
 							}
 						}
 					}
+					afterProcessFiles();
 					progIndicator.goAway();
 				}
 
@@ -406,20 +456,21 @@ protected String getImporterName(){
 		String [] exporterNames = new String[count];
 		exporterNames[0] = "NEXUS file";
 		count = 1;
+		int rememberedNumber = 0;
 		for (int i=0; i<fInterpreters.length; i++)
 			if (((FileInterpreterI)fInterpreters[i]).canImport()) {
 				exporterNames[count] = fInterpreters[i].getName();
+				if (exporterNames[count].equalsIgnoreCase(importerString))
+					rememberedNumber = count;
 				count++;
 			}
-
-		Choice exporterChoice = dialog.addPopUpMenu ("File Format", exporterNames, 0);
-		exporterChoice.select(importerString);
+		Choice exporterChoice = dialog.addPopUpMenu ("File Format", exporterNames, rememberedNumber);
 		dialog.addBlankLine();
 		dialog.completeAndShowDialog();
 		importerString = exporterChoice.getSelectedItem();
-
 		dialog.dispose();
 		dialog = null;
+		storePreferences();
 		return importerString;
 
 	}
diff --git a/Source/mesquite/io/InterpretTabbedCat/InterpretTabbedCat.java b/Source/mesquite/io/InterpretTabbedCat/InterpretTabbedCat.java
index 22cd4bbb0..42302613e 100644
--- a/Source/mesquite/io/InterpretTabbedCat/InterpretTabbedCat.java
+++ b/Source/mesquite/io/InterpretTabbedCat/InterpretTabbedCat.java
@@ -84,7 +84,7 @@ public void readFile(MesquiteProject mf, MesquiteFile file, String arguments) {
 							ic++;
 						else { //sc isn't tab; is name of ic'th character
 							if (data.getNumChars() <= ic) {
-								data.addParts(data.getNumChars()-1, 1);   // add a character if needed
+								data.addParts(data.getNumChars()-1, ic-data.getNumChars()+1);   // add characters if needed
 							}
 							data.setCharacterName(ic, sc);
 							if (st.hasMoreTokens())
diff --git a/Source/mesquite/io/lib/IOUtil.java b/Source/mesquite/io/lib/IOUtil.java
index f366d1173..09b5de178 100644
--- a/Source/mesquite/io/lib/IOUtil.java
+++ b/Source/mesquite/io/lib/IOUtil.java
@@ -96,7 +96,7 @@ public static String getMultipleModelRAxMLString(MesquiteModule mb, CharacterDat
 		boolean nucleotides = (data instanceof DNAData);
 		boolean protein = (data instanceof ProteinData);
 		String standardPart = "";
-		if (writeStandardPartition) {
+		if (writeStandardPartition && !partByCodPos) {
 			Listable[] partition = (Listable[])characterPartition.getProperties();
 			partition = data.removeExcludedFromListable(partition);
 			if (nucleotides) {
diff --git a/Source/mesquite/io/lib/InterpretFasta.java b/Source/mesquite/io/lib/InterpretFasta.java
index 53adf4f7b..395517388 100644
--- a/Source/mesquite/io/lib/InterpretFasta.java
+++ b/Source/mesquite/io/lib/InterpretFasta.java
@@ -184,6 +184,10 @@ public void processFileName(String fileName, CharacterData data, Taxa taxa, int
 		
 	}
 	
+	/*.................................................................................................................*/
+	public int getTaxonNumber(Taxa taxa, String token) {
+		return taxa.whichTaxonNumber(nameMatcherTask, token, false, false);   // checking to see if a taxon of that name already exists in the file
+	}
 	/*.................................................................................................................*/
 	public void readFileCore(Parser parser, MesquiteFile file, CharacterData data, Taxa taxa, int lastTaxonNumber, ProgressIndicator progIndicator, String arguments, boolean newFile, String fileName) {
 			boolean wassave = data.saveChangeHistory;
@@ -216,7 +220,7 @@ public void readFileCore(Parser parser, MesquiteFile file, CharacterData data, T
 				//parser.setPunctuationString(null);
 
 				token = subParser.getRemaining();  //taxon Name
-				taxonNumber = taxa.whichTaxonNumber(nameMatcherTask, token, false, false);   // checking to see if a taxon of that name already exists in the file
+				taxonNumber = getTaxonNumber(taxa, token);   // checking to see if a taxon of that name already exists in the file
 
 				if (!hasQueriedAboutSameNameTaxa && taxonNumber >= 0) {
 					if (!MesquiteThread.isScripting()){
@@ -299,7 +303,8 @@ else if (replaceDataOfTaxonWithSameNameInt==REPLACEIFEMPTYOTHERWISEIGNORE) {
 						recordAsNewlyAddedTaxon(taxa,taxonNumber);
 
 						checkMaximumTaxonFilled(taxonNumber);  // record this taxonNumber to see if it is the biggest yet.
-						t.setName(token);
+						if (!replace)  // we only set the name if we are not replacing the data of an already existing taxon
+							t.setName(token);
 						if (progIndicator!=null) {
 							progIndicator.setText("Reading taxon " + taxonNumber+": "+token);
 							CommandRecord.tick("Reading taxon " + taxonNumber+": "+token);
@@ -514,6 +519,9 @@ protected String getSupplementForTaxon(Taxa taxa, int it){
 		return "";
 	}
 	protected String getTaxonName(Taxa taxa, int it){
+		return getTaxonName(taxa, it, null);
+	}
+	protected String getTaxonName(Taxa taxa, int it, CharacterData data){
 		if (simplifyTaxonName)
 			return StringUtil.cleanseStringOfFancyChars(taxa.getTaxonName(it)+uniqueSuffix,false,true);
 		else 
@@ -561,7 +569,7 @@ public  StringBuffer getDataAsFileText(MesquiteFile file, CharacterData data) {
 
 					counter = 1;
 					outputBuffer.append(">");
-					outputBuffer.append(getTaxonName(taxa,it));
+					outputBuffer.append(getTaxonName(taxa,it, data));
 					String sup = getSupplementForTaxon(taxa, it);
 					if (StringUtil.notEmpty(sup))
 						outputBuffer.append(sup);
diff --git a/Source/mesquite/io/lib/InterpretHennig86Base.java b/Source/mesquite/io/lib/InterpretHennig86Base.java
index 56d5bab97..5d2879e96 100644
--- a/Source/mesquite/io/lib/InterpretHennig86Base.java
+++ b/Source/mesquite/io/lib/InterpretHennig86Base.java
@@ -463,6 +463,7 @@ public StringBuffer getDataAsFileText(MesquiteFile file, CharacterData data) {
 			writeTaxaWithAllMissing = file.writeTaxaWithAllMissing;
 			writeExcludedCharacters = file.writeExcludedCharacters;
 			fractionApplicable = file.fractionApplicable;
+			writeCharLabels = file.writeCharLabels;
 		}
 
 
@@ -473,7 +474,7 @@ public StringBuffer getDataAsFileText(MesquiteFile file, CharacterData data) {
 			dread.appendCommandToStringBuffer(outputBuffer, taxa, data, progIndicator);
 		else
 			xread.appendCommandToStringBuffer(outputBuffer, taxa, data, progIndicator);
-		if (catData==null || (catData.hasStateNames()|| data.characterNamesExist()))
+		if (writeCharLabels && (catData==null || (catData.hasStateNames()|| data.characterNamesExist())))
 			availableCommands[cnamesElement].appendCommandToStringBuffer(outputBuffer, taxa, data, progIndicator);
 
 		availableCommands[2].appendCommandToStringBuffer(outputBuffer, taxa, data, progIndicator);  //ccode
diff --git a/Source/mesquite/lib/Associable.java b/Source/mesquite/lib/Associable.java
index 834c814f7..d70d790a3 100644
--- a/Source/mesquite/lib/Associable.java
+++ b/Source/mesquite/lib/Associable.java
@@ -1022,8 +1022,19 @@ public void restoreToPreviousOrder(){
 			}
 		}
 	}
-	/*-----------------------------------------*/
+
+
+	MesquiteTimer t3 = new MesquiteTimer();
+	MesquiteTimer t4 = new MesquiteTimer();
+	MesquiteTimer t5 = new MesquiteTimer();
+	MesquiteTimer t6 = new MesquiteTimer();
+
+	/*-----------------------------------------*
 	public boolean swapParts(int first, int second){
+		return swapParts(first, second, true);
+	}
+	*/
+	public boolean swapParts(int first, int second, boolean notify){
 		if (first>numParts || first<0) 
 			return false;
 		if (second>numParts || second<0) 
diff --git a/Source/mesquite/lib/AssociableWithSpecs.java b/Source/mesquite/lib/AssociableWithSpecs.java
index 1744fc415..54d114fbb 100644
--- a/Source/mesquite/lib/AssociableWithSpecs.java
+++ b/Source/mesquite/lib/AssociableWithSpecs.java
@@ -176,19 +176,19 @@ public boolean moveParts(int starting, int num, int justAfter){
   		}
 		return true;
 	}
-	public boolean swapParts(int first, int second){
-		if (!super.swapParts(first, second))
+	public boolean swapParts(int first, int second, boolean notify){
+		if (!super.swapParts(first, second, notify))
 			return false;
   		if (specsVectors!=null){ //update size of specification sets
 	  		for (int i=0; i<specsVectors.size(); i++) {
 	  			SpecsSetVector sv = (SpecsSetVector)specsVectors.elementAt(i);
 	  			for (int j=0; j<sv.size(); j++) {
 	  				SpecsSet css = (SpecsSet)sv.elementAt(j);
-	  				css.swapParts(first, second);
+	  				css.swapParts(first, second, notify);
 	  			}
 	  			SpecsSet currentSS = sv.getCurrentSpecsSet();
 	  			if (currentSS!=null)
-	  				currentSS.swapParts(first, second);
+	  				currentSS.swapParts(first, second, notify);
 	  		}
   		}
 		return true;
diff --git a/Source/mesquite/lib/BitsSpecsSet.java b/Source/mesquite/lib/BitsSpecsSet.java
index 3a20fff79..d4c86c169 100644
--- a/Source/mesquite/lib/BitsSpecsSet.java
+++ b/Source/mesquite/lib/BitsSpecsSet.java
@@ -199,7 +199,7 @@ public boolean moveParts(int starting, int num, int justAfter){
 	}
 	/*.................................................................................................................*/
  	/** */
-	public boolean swapParts(int first, int second){  
+	public boolean swapParts(int first, int second, boolean notify){  
 		setDirty(true);
  		myBits.swapParts(first, second);
 		return true;
diff --git a/Source/mesquite/lib/CircleSymbol.java b/Source/mesquite/lib/CircleSymbol.java
index 93efe4ec9..123a3166b 100644
--- a/Source/mesquite/lib/CircleSymbol.java
+++ b/Source/mesquite/lib/CircleSymbol.java
@@ -100,7 +100,7 @@ else if (getFill()) {
 			g.setColor(fillColor);
 			GraphicsUtil.fillOval(g,x-symSize,y-symSize, symSize+symSize,symSize+symSize);
 		}
-		g.setColor(rimColor);
+		g.setColor(edgeColor);
 		GraphicsUtil.drawOval(g,x-symSize,y-symSize, symSize+symSize,symSize+symSize);
 	}
 	/*.................................................................................................................*/
diff --git a/Source/mesquite/lib/ExternalProcessManager.java b/Source/mesquite/lib/ExternalProcessManager.java
index 08162211b..94b330986 100644
--- a/Source/mesquite/lib/ExternalProcessManager.java
+++ b/Source/mesquite/lib/ExternalProcessManager.java
@@ -314,7 +314,12 @@ public boolean monitorAndCleanUpShell(ProgressIndicator progressIndicator){
 				boolean goodValue = goodExitValue(proc.exitValue(), true);
 				if (!goodValue && !ownerModule.isDoomed() && !watcher.userAborted()) {
 					String message = name + " quit, possibly because of an error ("+proc.exitValue()+"). Please examine StandardOutputFile and StandardErrorFile in the analysis directory for information.";
-					AlertWithLinkToDirectory alert = new AlertWithLinkToDirectory(ownerModule.containerOfModule(),"Error in executing "+name, message, directoryPath);
+					if (ownerModule.okToInteractWithUser(MesquiteModule.CAN_PROCEED_ANYWAY, "Error in execution")){
+						AlertWithLinkToDirectory alert = new AlertWithLinkToDirectory(ownerModule.containerOfModule(),"Error in executing "+name, message, directoryPath);
+					}
+					else {
+						MesquiteMessage.warnUser(message);
+					}
 				}
 				badExitCode = !goodValue;
 				return goodValue;
diff --git a/Source/mesquite/lib/FileElement.java b/Source/mesquite/lib/FileElement.java
index ce7eb1257..01e06413a 100644
--- a/Source/mesquite/lib/FileElement.java
+++ b/Source/mesquite/lib/FileElement.java
@@ -246,7 +246,6 @@ public void showMe(){
 	}
 	public MesquiteModule show(){
 		ElementManager manager = getManager();
-		
 		if (manager!=null)
 			return manager.showElement(this);
 		return null;
@@ -461,7 +460,6 @@ public void setManager(ElementManager e){
 	/*.................................................................................................................*/
 	/** Returns the FileElement's managing module */
 	public ElementManager getManager(){
-
 		if (elementManager==null){//IF MANAGER NULL then find one
 			if (file != null && project == null)
 				project = file.getProject();
@@ -469,7 +467,14 @@ public ElementManager getManager(){
 				return null;
 			if (project.getCoordinatorModule()==null)
 				return null;
-			elementManager = project.getCoordinatorModule().findElementManager(getClass());
+			Class c = getClass();
+			if (this == project.datas)
+				c = mesquite.lib.characters.CharacterData.class;
+			else if (this == project.getTreeVectors())
+				c = TreeVector.class;
+			else if (this == project.taxas)
+				c = Taxa.class;
+			elementManager = project.getCoordinatorModule().findElementManager(c);
 		}
 		return elementManager;
 	}
diff --git a/Source/mesquite/lib/FillableMesquiteSymbol.java b/Source/mesquite/lib/FillableMesquiteSymbol.java
index 5f3b5f9ab..86a60a30f 100644
--- a/Source/mesquite/lib/FillableMesquiteSymbol.java
+++ b/Source/mesquite/lib/FillableMesquiteSymbol.java
@@ -24,7 +24,13 @@ public abstract class FillableMesquiteSymbol extends MesquiteSymbol {
 	Checkbox fillBox = null;
 	protected boolean fill=true;
 	Color fillColor = Color.black;
-	Color rimColor = Color.black;
+	
+	Checkbox edgeWhiteBox = null;
+	Color edgeColor = Color.white;
+	protected boolean edgeWhite=true;
+	IntegerField edgeWidthField = null;
+	private int edgeWidth = 1;
+	
 	/**sets whether to fill the symbol or not*/
 	public void setFill(boolean fill){
 		this.fill = fill;
@@ -33,40 +39,92 @@ public void setFill(boolean fill){
 	public boolean getFill(){
 		return fill;
 	}
+	/**sets whether the edge of the symbol is white (as opposed to black)*/
+	public void setEdgeWhite(boolean edgeWhite){
+		this.edgeWhite = edgeWhite;
+		if (edgeWhite)
+			edgeColor = Color.white;
+		else
+			edgeColor = Color.black;
+	}
+	/**gets whether the edge of the symbol is white or not*/
+	public boolean getEdgeWhite(){
+		return edgeWhite;
+	}
+	/**sets the thickness of the edge*/
+	public void setEdgeWidth(int width){
+		this.edgeWidth = width;
+	}
+	/**gets whether to fill the symbol or not*/
+	public int getEdgeWidth(){
+		return edgeWidth;
+	}
+
 	/**gets the NEXUS commands to specify the options specific to this tool*/
 	public String getBasicNexusOptions(){
+		String s = "";
 		if (getFill())
-			return " FILL ";
+			s = " FILL ";
 		else
-			return " OPEN ";
+			s = " OPEN ";
+		if (getEdgeWhite())
+			s += "EDGEWHITE ";
+		else
+			s +="EDGEBLACK ";
+		s += "EDGEWIDTH=" + getEdgeWidth();
+		return s;
+		
 	}
 	/*.................................................................................................................*/
 	public void  setToCloned(MesquiteSymbol cloned){
 		super.setToCloned(cloned);
 		setFill(((FillableMesquiteSymbol)cloned).getFill());
+		setEdgeWidth(((FillableMesquiteSymbol)cloned).getEdgeWidth());
+		setEdgeWhite(((FillableMesquiteSymbol)cloned).getEdgeWhite());
 	}
 	/*.................................................................................................................*/
 	public void addDialogElements(ExtensibleDialog dialog, boolean includeSize){
 		super.addDialogElements(dialog, includeSize);
 		fillBox = dialog.addCheckBox("filled", fill);
+		edgeWhiteBox = dialog.addCheckBox("edge white", edgeWhite);
+		edgeWidthField = dialog.addIntegerField("thickness of edge", edgeWidth, 5, 1, 20000);
 	}
 	/*.................................................................................................................*/
 	public void getDialogOptions(){
 		super.getDialogOptions();
 		fill = fillBox.getState();
+		setEdgeWhite(edgeWhiteBox.getState());
+		setEdgeWidth(edgeWidthField.getValue());
 	}
 	/*.................................................................................................................*/
 	public void processSubcommand(String token, Parser subcommands){
 		super.processSubcommand(token, subcommands);
-		if (token.equalsIgnoreCase("FILL"))
+		if (token.equalsIgnoreCase("FILL")) {
 			setFill(true);
-		else if (token.equalsIgnoreCase("OPEN"))
+		}
+		else if (token.equalsIgnoreCase("OPEN")) {
 			setFill(false);
+		}	
+		else if (token.equalsIgnoreCase("EDGEWHITE")) {
+			setEdgeWhite(true);
+		}
+		else if (token.equalsIgnoreCase("EDGEBLACK")) {
+			setEdgeWhite(false);
+		}
+		else if (token.equalsIgnoreCase("EDGEWIDTH")) {
+			token = subcommands.getNextToken(); // should be "=";
+			token = subcommands.getNextToken(); // value;
+			setEdgeWidth(MesquiteInteger.fromString(token));
+		}
 	}
 	/**sets fill color*/
 	public void setFillColor(Color color){
 		this.fillColor = color;
 	}
+	/**sets edge color*/
+	public void setEdgeColor(Color color){
+		this.edgeColor = color;
+	}
 	/**sets fill color*/
 	public void setColor(Color color){
 		this.fillColor = color;
@@ -136,9 +194,9 @@ else if (getFill()) {
 						g.setColor(fillColor);
 						GraphicsUtil.fill(g,poly);
 					}
-					g.setColor(rimColor);
+					g.setColor(edgeColor);
 
-					GraphicsUtil.draw(g,poly);
+					GraphicsUtil.draw(g,poly, edgeWidth);
 				}
 				g2.setTransform(saveTransform);
 			}
diff --git a/Source/mesquite/lib/GraphicsUtil.java b/Source/mesquite/lib/GraphicsUtil.java
index 4664d30c6..a36daa8f1 100644
--- a/Source/mesquite/lib/GraphicsUtil.java
+++ b/Source/mesquite/lib/GraphicsUtil.java
@@ -132,11 +132,17 @@ public static void fill(Graphics g, Shape shape) {
 	}
 	/*_________________________________________________*/
 	public static void draw(Graphics g, Shape shape) {
+		draw(g,shape,1);
+	}
+	/*_________________________________________________*/
+	public static void draw(Graphics g, Shape shape, int strokeWidth) {
 		if (!(g instanceof Graphics2D))
 			return;
 		Graphics2D g2 = (Graphics2D)g;
 		g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+		g2.setStroke(new BasicStroke(strokeWidth));
 		g2.draw(shape);
+		g2.setStroke(new BasicStroke(1));
 	}
 
 	/*_________________________________________________*/
diff --git a/Source/mesquite/lib/GroupLabel.java b/Source/mesquite/lib/GroupLabel.java
index b150d79ae..c100f6bf2 100644
--- a/Source/mesquite/lib/GroupLabel.java
+++ b/Source/mesquite/lib/GroupLabel.java
@@ -10,14 +10,14 @@
 
 This source code and its compiled class files are free and modifiable under the terms of 
 GNU Lesser General Public License.  (http://www.gnu.org/copyleft/lesser.html)
-*/
+ */
 package mesquite.lib;
 
 import java.awt.*;
 
 import mesquite.lib.duties.*;
 
-	
+
 /* ======================================================================== */
 /** DOCUMENT.*/
 public class GroupLabel extends FileElement {
@@ -44,7 +44,7 @@ public GroupLabel() {
 			tS = -tS;
 		tS = tS % 25;
 		color = new Color(Color.HSBtoRGB((float)((25-tS) * 0.8 /25),(float)1.0,(float)1.0));
-		*/
+		 */
 		color = null;
 	}
 	public static boolean supportsSymbols() {
@@ -82,8 +82,10 @@ public boolean colorSet(){
 	/*.................................................................................................................*/
 	public void setSymbol(MesquiteSymbol symbol){
 		this.symbol = symbol;
-		symbol.setColor(getColor());
-		this.symbol.setColor(getColor());
+		if (symbol != null){
+			symbol.setColor(getColor());
+			this.symbol.setColor(getColor());
+		}
 		symbolWasSet = true;
 		notifyListeners(this, new Notification(MesquiteListener.DATA_CHANGED));
 	}
@@ -101,7 +103,7 @@ public boolean isRecentlyModified() {
 	public void setRecentlyModified(boolean recentlyModified) {
 		this.recentlyModified = recentlyModified;
 	}
-	
+
 	/*.................................................................................................................*/
 }
 
diff --git a/Source/mesquite/lib/ListableVector.java b/Source/mesquite/lib/ListableVector.java
index 105810f04..bbf5a2be0 100644
--- a/Source/mesquite/lib/ListableVector.java
+++ b/Source/mesquite/lib/ListableVector.java
@@ -373,8 +373,13 @@ public void removeAllElements(boolean notify){
 		if (notify)
 			notifyListeners(this, new Notification(MesquiteListener.PARTS_DELETED));
 	}
-	/*...........................................................*/
+	/*...........................................................*
 	public boolean swapParts(int first, int second) {
+		return swapParts(first, second, true);
+	}
+	*/
+	
+	public boolean swapParts(int first, int second, boolean notify) {
 		if (first<0 || first>=size() || second<0 || second>=size()) 
 			return false;
 		mesquite.lib.duties.ElementManager m = null;
@@ -385,9 +390,9 @@ public boolean swapParts(int first, int second) {
 		Object objSecond = vec.elementAt(second);
 		vec.setElementAt(objSecond, first);
 		vec.setElementAt(objFirst, second);
-		if (m != null)
+		if (notify && m != null)
 			m.elementsReordered(this);
-		return super.swapParts(first, second);
+		return super.swapParts(first, second, notify);
 		
 	}
 	/*...........................................................*/
diff --git a/Source/mesquite/lib/MesquiteDialog.java b/Source/mesquite/lib/MesquiteDialog.java
index b6980b62d..ebd1309d6 100644
--- a/Source/mesquite/lib/MesquiteDialog.java
+++ b/Source/mesquite/lib/MesquiteDialog.java
@@ -75,12 +75,15 @@ else if (parent instanceof MesquiteWindow){
 					MesquiteWindow mw = ((MesquiteWindow)parent);
 					if (!mw.isVisible() && mw.getOwnerModule() != null)
 						mw = mw.getOwnerModule().visibleContainerOfModule();
-					if (mw == null)
+					if (mw == null) {
 						f = MesquiteWindow.dialogAnchor;
+					}
 					else
 						f = mw.getParentFrame();
 				}
 			}
+			if (f == MesquiteWindow.dialogAnchor && (MesquiteTrunk.debugMode))
+				MesquiteMessage.printStackTrace("@@@@@@@@@@@DIALOG ANCHOR USED FOR " + title); //Debugg.println
 
 			parentDialog = new MesquiteDialogParent(f, title, !usingWizard);
 			//parentDialog = new MesquiteDialogParent(MesquiteWindow.dialogAnchor, title, !usingWizard);
diff --git a/Source/mesquite/lib/MesquiteFileUtil.java b/Source/mesquite/lib/MesquiteFileUtil.java
index 061c75961..613049103 100644
--- a/Source/mesquite/lib/MesquiteFileUtil.java
+++ b/Source/mesquite/lib/MesquiteFileUtil.java
@@ -38,6 +38,15 @@ public static String createDirectoryForFiles(MesquiteModule module, boolean askF
 	public static final int BESIDE_HOME_FILE = 1;
 	public static final int ASK_FOR_LOCATION = 2;
 	/*.................................................................................................................*/
+	public static String pathForFiles(String enclosingDirectoryPath, String name, String suffix, boolean createUniqueDatedName) {
+		String path = enclosingDirectoryPath + StringUtil.cleanseStringOfFancyChars(name, false, true);
+		if (createUniqueDatedName) {
+			path+= "-" + StringUtil.getDateDayOnly() + suffix;
+			path = MesquiteFile.getUniqueNumberedPath(path);
+		}
+		return path;
+	}
+	/*.................................................................................................................*/
 	public static String createDirectoryForFiles(MesquiteModule module, int location, String name, String suffix, boolean createUniqueDatedName) {
 		MesquiteBoolean directoryCreated = new MesquiteBoolean(false);
 		String rootDir = null;
@@ -45,11 +54,7 @@ public static String createDirectoryForFiles(MesquiteModule module, int location
 			rootDir = module.createEmptySupportDirectory(directoryCreated) + MesquiteFile.fileSeparator;  //replace this with current directory of file
 		else if (location == BESIDE_HOME_FILE) {
 			String dir = module.getProject().getHomeFile().getDirectoryName();
-			String path = dir + StringUtil.cleanseStringOfFancyChars(name, false, true);
-			if (createUniqueDatedName) {
-				path+= "-" + StringUtil.getDateDayOnly() + suffix;
-				path = MesquiteFile.getUniqueNumberedPath(path);
-			}
+			String path = pathForFiles(dir, name, suffix, createUniqueDatedName);
 			File f = new File(path);
 			boolean b = f.mkdir();
 			directoryCreated.setValue(b);
@@ -57,12 +62,19 @@ else if (location == BESIDE_HOME_FILE) {
 				rootDir = path + MesquiteFile.fileSeparator;
 		}
 		if (!directoryCreated.getValue()) {
-			rootDir = MesquiteFile.chooseDirectory("Choose folder for storing "+name+" files");
-			if (rootDir==null) {
+			String path = MesquiteFile.chooseDirectory("Choose folder for storing "+name+" files");
+			if (path==null) {
 				MesquiteMessage.discreetNotifyUser("Sorry, directory for storing "+name+" files could not be created.");
 				return null;
-			} else
-				rootDir += MesquiteFile.fileSeparator;
+			} else {
+				path += MesquiteFile.fileSeparator;
+				path = pathForFiles(path, name, suffix, createUniqueDatedName);
+				File f = new File(path);
+				boolean b = f.mkdir();
+				directoryCreated.setValue(b);
+				if (b)
+					rootDir = path + MesquiteFile.fileSeparator;
+			}
 		}
 		return rootDir;
 	}
diff --git a/Source/mesquite/lib/MesquiteFrame.java b/Source/mesquite/lib/MesquiteFrame.java
index 2496cd299..7d18a623a 100644
--- a/Source/mesquite/lib/MesquiteFrame.java
+++ b/Source/mesquite/lib/MesquiteFrame.java
@@ -356,6 +356,9 @@ else if (project.hasName())
 			setTitle(project.getHomeFileName());
 
 
+	}
+	public MesquiteWindow getFrontWindow(){
+		return frontWindow;
 	}
 	public void fixFrontness(){
 		MesquiteWindow w = frontMostInLocation(MesquiteFrame.POPTILE);
diff --git a/Source/mesquite/lib/MesquiteModule.java b/Source/mesquite/lib/MesquiteModule.java
index bebb30155..54a9b997c 100644
--- a/Source/mesquite/lib/MesquiteModule.java
+++ b/Source/mesquite/lib/MesquiteModule.java
@@ -67,12 +67,12 @@ public abstract class MesquiteModule extends EmployerEmployee implements Command
 	/*.................................................................................................................*/
 	/** returns build date of the Mesquite system (e.g., "22 September 2003") */
 	public final static String getBuildDate() {
-		return "27 December 2018";
+		return "26 December 2019";
 	}
 	/*.................................................................................................................*/
 	/** returns version of the Mesquite system */
 	public final static String getMesquiteVersion() {
-		return "3.6";
+		return "3.61";
 	}
 	/*.................................................................................................................*/
 	/** returns letter in the build number of the Mesquite system (e.g., "e" of "e58") */
@@ -85,7 +85,7 @@ public final static String getBuildLetter() {
 	public final static int getBuildNumber() {
 		//as of 26 Dec 08, build naming changed from letter + number to just number.  Accordingly j105 became 473, based on
 		// highest build numbers of d51+e81+g97+h66+i69+j105 + 3 for a, b, c
-		return 917;  
+		return 927;  
 	}
 	//0.95.80    14 Mar 01 - first beta release 
 	//0.96  2 April 01 beta  - second beta release
@@ -137,6 +137,7 @@ public final static int getBuildNumber() {
 	//3.50  = 888 released 4 May 2O18
 	//3.51  = 898 released 28 June 2O18
 	//3.6  = 917 released 27 Dec 2O18
+	//3.61  = 927 released 26 Dec 2O19
 	/*.................................................................................................................*/
 	/** returns a string if this is a special version of Mesquite */
 	public final static String getSpecialVersion() {
diff --git a/Source/mesquite/lib/MesquiteProject.java b/Source/mesquite/lib/MesquiteProject.java
index 97c840dd5..2d0eee4a0 100644
--- a/Source/mesquite/lib/MesquiteProject.java
+++ b/Source/mesquite/lib/MesquiteProject.java
@@ -81,15 +81,23 @@ public MesquiteProject(FileCoordinator ownerModule) {
 		this.ownerModule = ownerModule;
 		startupTime = System.currentTimeMillis();
 		datas = new ListableVector();  
+		datas.setProject(this);
+		datas.setName("Character Matrices");
 		taxas = new ListableVector();  
+		taxas.setProject(this);
+		taxas.setName("Taxa Blocks");
 		charModels = new ModelVector();
+		charModels.setProject(this);
 		datas.addListener(this);
 		taxas.addListener(this);
 		charModels.addListener(this);
 		modelListener = new CentralModelListener();
 		treeVectors = new ListableVector();
+		treeVectors.setProject(this);
+		treeVectors.setName("Tree Blocks");
 		otherElements = new ListableVector();
 		otherElements.setName("other file elements in project");
+		otherElements.setProject(this);
 		files = new ListableVector();
 		nexusBlocks = new ListableVector( 1);
 		idNumber = totalCreated;
@@ -275,29 +283,26 @@ public TreeVector getTreesByID(long id) {
 		return null;
 	}
 
+	/*.................................................................................................................*/
+	/** returns the number of Tree Vectors */
+	public int getNumberTreeVectors(Taxa t) {
+		int count = 0;
+		for (int i = 0; i<treeVectors.size(); i++){
+			TreeVector trees = (TreeVector)treeVectors.elementAt(i);
+			if (trees.getTaxa() == t)
+				count++;
+		}
+		return count;
+	}
 	/*.................................................................................................................*/
 	/** returns the number of Tree Vectors */
 	public int getNumberTreeVectors() {
 		return treeVectors.size();
-		/*ListableVector v = new ListableVector();		
-		for (int i=0; i<getNumberOfFileElements(TreeVector.class); i++) {
-			TreeVector trees = (TreeVector)getFileElement(TreeVector.class, i);
-			if (!trees.isDoomed())
-				v.addElement(trees, false);
-		}
-		return v;*/
 	}
 	/*.................................................................................................................*/
 	/** returns the Tree Vectors */
 	public ListableVector getTreeVectors() {
 		return treeVectors;
-		/*ListableVector v = new ListableVector();		
-		for (int i=0; i<getNumberOfFileElements(TreeVector.class); i++) {
-			TreeVector trees = (TreeVector)getFileElement(TreeVector.class, i);
-			if (!trees.isDoomed())
-				v.addElement(trees, false);
-		}
-		return v;*/
 	}
 
 	/*.................................................................................................................*/
@@ -813,6 +818,9 @@ else if (element instanceof CharacterModel) {
 	/*.................................................................................................................*/
 	/** DOCUMENT */
 	public void removeFileElement(FileElement element) {
+		removeFileElement(element, true);
+	}
+	public void removeFileElement(FileElement element, boolean notify) {
 		if (element==null)
 			return;
 		element.removeListener(this);
@@ -849,7 +857,8 @@ else if (element instanceof CharacterModel) {
 				otherElements.removeElement(element, true);
 			//otherElements.notifyListenersOfDisposed(element);
 		}
-		notifyListeners(this, new Notification(MesquiteListener.PARTS_DELETED));
+		if (notify)
+			notifyListeners(this, new Notification(MesquiteListener.PARTS_DELETED));
 		//TODO: shouldn't broadcase of deletion be here?
 	}
 	/*.................................................................................................................*/
diff --git a/Source/mesquite/lib/MesquiteTextWindow.java b/Source/mesquite/lib/MesquiteTextWindow.java
index 1270b5e70..5a549cc25 100644
--- a/Source/mesquite/lib/MesquiteTextWindow.java
+++ b/Source/mesquite/lib/MesquiteTextWindow.java
@@ -108,7 +108,9 @@ public String getText() {
 		return tA.getText();
 	}
 	public void focusGained(FocusEvent e){
-
+		if (!isFrontMostWindow()){
+			getParentFrame().setAsFrontWindow(this);
+		}
 	}
 	public void focusLost(FocusEvent e){
 
diff --git a/Source/mesquite/lib/MesquiteWindow.java b/Source/mesquite/lib/MesquiteWindow.java
index e117c73d6..5d02d0f1b 100644
--- a/Source/mesquite/lib/MesquiteWindow.java
+++ b/Source/mesquite/lib/MesquiteWindow.java
@@ -36,6 +36,9 @@ public abstract class MesquiteWindow implements Listable, Commandable, OwnedByMo
 	public MesquiteMenuBar menuBar;
 	public static Vector classesCreated, countsOfClasses, countsOfClassesFinalized; //to detect memory leaks
 
+	public static Vector delayedRepaintQueue = new Vector(); //to be repainted in about 1-2 seconds (initially, to work around graphics bug affecting Chromaseq
+	public long drqTime = 0;
+	
 	public boolean resetMenuPending = false;
 	public int painting = 0;
 	public boolean disposing = false;
@@ -347,6 +350,14 @@ public void resetTime(){
 		if (windowTimer!=null)
 			windowTimer.resetLastTime();
 	}
+	
+	public void addToDelayedRepaintQueue(long extraDelayTime){ 
+		// best to add extraDelayTime of at least 500 ms in case happens to be put on queue just before the thread looks for windows for delayed repainting
+		drqTime = System.currentTimeMillis() + extraDelayTime;
+		delayedRepaintQueue.addElement(this); 
+		//for execution, search for delayedRepaintQueue in ClockWatcherThread
+	}
+	
 	public void logTime(String message){
 		if (windowTimer!=null)
 			if (!StringUtil.blank(message))
@@ -449,6 +460,9 @@ public void setParentFrame(MesquiteFrame f){
 	public boolean isFrontMostInLocation(){
 		return parentFrame.frontMostInLocation(getTileLocation()) == this;
 	}
+	public boolean isFrontMostWindow(){
+		return parentFrame.getFrontWindow() == this;
+	}
 	public void setAsPrimaryMesquiteWindow(boolean p){
 		if (parentFrame != null)
 			parentFrame.setAsPrimaryMesquiteFrame(p);
diff --git a/Source/mesquite/lib/MiniScrollButton.java b/Source/mesquite/lib/MiniScrollButton.java
index 81654b632..b12e86655 100644
--- a/Source/mesquite/lib/MiniScrollButton.java
+++ b/Source/mesquite/lib/MiniScrollButton.java
@@ -56,9 +56,57 @@ public MiniScrollButton (MiniScroll miniScroll, int orientation, String itemName
 		this.miniScroll = miniScroll;
 		this.itemName = itemName;
 		arrowPoly= new Polygon();
-		arrowPoly.xpoints = new int[4];
-		arrowPoly.ypoints = new int[4];
-		if (orientation==LEFT) {
+		arrowPoly.xpoints = new int[7];
+		arrowPoly.ypoints = new int[7];
+		int wid = 16;
+		int hlf = 6;
+		int pg = 4;
+		int cg = 4;
+		if (orientation==LEFT) { //made more inclusive Dec 2019
+			arrowPoly.npoints=0;
+			arrowPoly.addPoint(0, hlf);
+			arrowPoly.addPoint(wid-cg, 0);
+			arrowPoly.addPoint(wid, 0);
+			arrowPoly.addPoint(wid, wid);
+			arrowPoly.addPoint(wid-cg, wid);
+			arrowPoly.addPoint(0, hlf+pg);
+			arrowPoly.addPoint(0, hlf);
+			arrowPoly.npoints=7;
+		}
+		else if (orientation == RIGHT){
+			arrowPoly.npoints=0;
+			arrowPoly.addPoint(0, 0);
+			arrowPoly.addPoint(cg, 0);
+			arrowPoly.addPoint(wid, hlf);
+			arrowPoly.addPoint(wid, hlf+pg);
+			arrowPoly.addPoint(cg, wid);
+			arrowPoly.addPoint(0, wid);
+			arrowPoly.addPoint(0, 0);
+			arrowPoly.npoints=7;
+		}
+		else if (orientation==UP) {
+			arrowPoly.npoints=0;
+			arrowPoly.addPoint(hlf, 0);
+			arrowPoly.addPoint(hlf+pg, 0);
+			arrowPoly.addPoint(wid, wid-cg);
+			arrowPoly.addPoint(wid, wid);
+			arrowPoly.addPoint(0, wid);
+			arrowPoly.addPoint(0, wid-cg);
+			arrowPoly.addPoint(hlf, 0);
+			arrowPoly.npoints=7;
+		}
+		else if (orientation == DOWN){
+			arrowPoly.npoints=0;
+			arrowPoly.addPoint(0, 0);
+			arrowPoly.addPoint(wid, 0);
+			arrowPoly.addPoint(wid, cg);
+			arrowPoly.addPoint(hlf+pg, wid);
+			arrowPoly.addPoint(hlf, wid);
+			arrowPoly.addPoint(0, cg);
+			arrowPoly.addPoint(0, 0);
+			arrowPoly.npoints=7;
+		}
+/*		if (orientation==LEFT) {
 			arrowPoly.npoints=0;
 			arrowPoly.addPoint(1, 7);
 			arrowPoly.addPoint(15, 15);
@@ -90,6 +138,7 @@ else if (orientation == DOWN){
 			arrowPoly.addPoint(7, 15);
 			arrowPoly.npoints=4;
 		}
+		*/
 		setBackground(ColorTheme.getInterfaceBackground());
 		setBounds(0,0,16,16);
 	}
@@ -169,7 +218,6 @@ else if (disabled)
 		MesquiteWindow.uncheckDoomed(this);
 	}
   	public void mouseDown (int modifiers, int clickCount, long when, int x, int y, MesquiteTool tool) {
-		
 		Graphics g=getGraphics();
 		if (g == null)
 			return;
diff --git a/Source/mesquite/lib/NumSpecsSet.java b/Source/mesquite/lib/NumSpecsSet.java
index 37e806426..d2bcb0a6e 100644
--- a/Source/mesquite/lib/NumSpecsSet.java
+++ b/Source/mesquite/lib/NumSpecsSet.java
@@ -168,7 +168,7 @@ public boolean moveParts(int starting, int num, int justAfter){
 	}
 	/*.................................................................................................................*/
  	/** */
-	public boolean swapParts(int first, int second){  
+	public boolean swapParts(int first, int second, boolean notify){  
 		setDirty(true);
  		nums.swapParts(first, second);
 		return true;
diff --git a/Source/mesquite/lib/ObjectSpecsSet.java b/Source/mesquite/lib/ObjectSpecsSet.java
index e81878788..0ce6a068b 100644
--- a/Source/mesquite/lib/ObjectSpecsSet.java
+++ b/Source/mesquite/lib/ObjectSpecsSet.java
@@ -143,7 +143,7 @@ public boolean deleteParts(int starting, int num){
 		return true;
 	}
 	/*...........................................................*/
-	public boolean swapParts( int first, int second) {
+	public boolean swapParts( int first, int second, boolean notify) {
 		if (first<0 || first>=properties.length || second<0 || second>=properties.length) 
 			return false;
 		setDirty(true);
diff --git a/Source/mesquite/lib/Parser.java b/Source/mesquite/lib/Parser.java
index b4ef25a2d..74be37717 100644
--- a/Source/mesquite/lib/Parser.java
+++ b/Source/mesquite/lib/Parser.java
@@ -523,7 +523,7 @@ else if (line.equals(""))
 			return "";
 		if (pos.getValue() >= line.length())
 			return null;
-		char c=getNextCharRaw();  //Debugg.println(this had used NEXUS characters, i.e. skipped brackets) OK to have changed?
+		char c=getNextCharRaw();  
 		buffer.setLength(0);
 
 		while (!lineEndCharacter(c) && pos.getValue()<=line.length() && c!=(char)0) {  
diff --git a/Source/mesquite/lib/StringUtil.java b/Source/mesquite/lib/StringUtil.java
index 80a882ee6..40b3b53d3 100644
--- a/Source/mesquite/lib/StringUtil.java
+++ b/Source/mesquite/lib/StringUtil.java
@@ -188,6 +188,13 @@ public static String getDateTime() {
 		return getDateTime(dnow);
 	}
 	/*.................................................................................................................*/
+	public static String getDateTimeWithSeconds() {
+		long t = System.currentTimeMillis();
+		Date dnow = new Date(t);
+		SimpleDateFormat sdf = new SimpleDateFormat("dd MMMMM yyyy,  HH:mm:ss.SSS z");
+		return sdf.format(dnow);
+	}
+	/*.................................................................................................................*/
 	public static String getOutputFileStamp(MesquiteModule m) {
 		StringBuffer sb = new StringBuffer();
 		sb.append("Mesquite version " + m.getMesquiteVersion() + m.getBuildVersion() + "\n");
diff --git a/Source/mesquite/lib/Taxa.java b/Source/mesquite/lib/Taxa.java
index 29812903f..c23c6fdd8 100644
--- a/Source/mesquite/lib/Taxa.java
+++ b/Source/mesquite/lib/Taxa.java
@@ -909,6 +909,11 @@ public boolean deleteParts(int starting, int num) {
 		return true;
 	}
 
+	/*-----------------------------------------------------------*/
+	/**Swaps taxa first and second.*/
+	public boolean swapParts(int first, int second){
+		return swapParts(first, second, true);
+	}
 	/* ................................................................................................................. */
 	/** Swaps taxa first and second */
 	public boolean swapTaxa(int first, int second, boolean notify) {
@@ -919,7 +924,7 @@ public boolean swapTaxa(int first, int second, boolean notify) {
 			return false;
 		if (inhibitEdit>0)
 			return false;
-		swapParts(first, second);
+		swapParts(first, second, notify);
 		notifyOfChangeLowLevel(MesquiteListener.PARTS_SWAPPED, first, second, 0);  
 		inFlux = true;
 		/*
@@ -951,7 +956,7 @@ public final boolean moveTaxa(int first, int num, int justAfter, boolean notify)
 	}
 
 	/* ........................................................... */
-	public boolean swapParts(int first, int second) {
+	public boolean swapParts(int first, int second, boolean notify) {
 		if (first < 0 || first >= taxon.length || second < 0
 				|| second >= taxon.length)
 			return false;
@@ -963,7 +968,7 @@ public boolean swapParts(int first, int second) {
 		Taxon temp = taxon[first];
 		taxon[first] = taxon[second];
 		taxon[second] = temp;
-		boolean success = super.swapParts(first, second);
+		boolean success = super.swapParts(first, second, notify);
 		taxon[first].setIndex(first);
 		taxon[second].setIndex(second);
 		inFlux = false;
diff --git a/Source/mesquite/lib/TaxaBitsSet.java b/Source/mesquite/lib/TaxaBitsSet.java
index 393481c6e..c0beabfd1 100644
--- a/Source/mesquite/lib/TaxaBitsSet.java
+++ b/Source/mesquite/lib/TaxaBitsSet.java
@@ -50,9 +50,9 @@ public boolean moveParts(int first, int num, int justAfter){
 		return super.moveParts(first, num, justAfter);
 	}
 	/*.................................................................................................................*/
-	public boolean swapParts(int first, int second){  
+	public boolean swapParts(int first, int second, boolean notify){  
 		setDirty(true);
-		return super.swapParts(first, second);
+		return super.swapParts(first, second, notify);
 	}
 	/*.................................................................................................................*/
 	public String getStringList(String delimiter, TaxonNamer namer, boolean justFirst){  
diff --git a/Source/mesquite/lib/TaxaSpecsSet.java b/Source/mesquite/lib/TaxaSpecsSet.java
index d7313913c..57e936851 100644
--- a/Source/mesquite/lib/TaxaSpecsSet.java
+++ b/Source/mesquite/lib/TaxaSpecsSet.java
@@ -30,7 +30,7 @@ public interface TaxaSpecsSet extends Listable {
 	public boolean moveParts(int first, int num, int justAfter);
 	/*.................................................................................................................*/
 	/*.................................................................................................................*/
-	public boolean swapParts(int first, int second);
+	public boolean swapParts(int first, int second, boolean notify);
 	
 	public Taxa getTaxa();
 }
diff --git a/Source/mesquite/lib/TaxaStringsSet.java b/Source/mesquite/lib/TaxaStringsSet.java
index 74da0c0ac..7f698c1e6 100644
--- a/Source/mesquite/lib/TaxaStringsSet.java
+++ b/Source/mesquite/lib/TaxaStringsSet.java
@@ -73,9 +73,9 @@ public boolean moveParts(int first, int num, int justAfter){
 		return super.moveParts(first, num, justAfter);
 	}
 	/*.................................................................................................................*/
-	public boolean swapParts(int first, int second){  
+	public boolean swapParts(int first, int second, boolean notify){  
 		setDirty(true);
-		return super.swapParts(first, second);
+		return super.swapParts(first, second, notify);
 	}
 }
 
diff --git a/Source/mesquite/lib/TaxaTreeDisplay.java b/Source/mesquite/lib/TaxaTreeDisplay.java
index 50c4065cd..78ba8ee1f 100644
--- a/Source/mesquite/lib/TaxaTreeDisplay.java
+++ b/Source/mesquite/lib/TaxaTreeDisplay.java
@@ -181,6 +181,42 @@ public void pleaseUpdate(boolean resetElements) {  //TODO: this whole system nee
 	public void repaint(boolean resetElements){
 		repaint();
 	}
+	public String repaintChain  = "";
+	public long chainResetTime = -1;
+	public boolean chainEnabled = false; 
+	public void enableChain(){
+		chainEnabled = true;
+	}
+	public void resetChain(){
+		if (chainEnabled == false)
+			return;
+		repaintChain = "";
+		chainResetTime = -1;
+	}
+	public void restartChain(String s){
+		if (chainEnabled == false)
+			return;
+		repaintChain = s;
+		chainResetTime = System.currentTimeMillis();
+	}
+	public void addToChain(String s){
+		if (chainEnabled == false)
+			return;
+		if (chainResetTime <0) //hasn't yet started
+			return;		
+		repaintChain = repaintChain + "\n" + s;
+	}
+	public void reportChain(String s){
+		if (chainEnabled == false)
+			return;
+		if (chainResetTime <0) //hasn't yet started
+			return;
+		repaintChain = repaintChain + "\n" + s;
+		MesquiteMessage.println("@@@@@@@@\nTime since tree changed in tree window " + ((System.currentTimeMillis()-chainResetTime)/1000.0) + " seconds");
+		MesquiteMessage.println(repaintChain);
+		resetChain();
+	}
+	
 	public void repaint() {  //TODO: this whole system needs revamping.  
 		if (!isVisible())
 			return;
@@ -195,6 +231,8 @@ public void repaint() {  //TODO: this whole system needs revamping.
 		}
 		repaintsPending++;
 		if (repaintsPending<=1){
+			if (MesquiteTrunk.debugMode)
+				addToChain("TTD-repaintCalled " + repaintsPending + "  " + StringUtil.getDateTimeWithSeconds()); 
 			super.repaint();
 			crossDrawn=false;
 		}
diff --git a/Source/mesquite/lib/TreeDisplay.java b/Source/mesquite/lib/TreeDisplay.java
index 0f8e4ad87..cd31874b5 100644
--- a/Source/mesquite/lib/TreeDisplay.java
+++ b/Source/mesquite/lib/TreeDisplay.java
@@ -198,8 +198,11 @@ public void setTree(Tree tree) {
 		if (tree!=null && tree.getTaxa() != taxa)
 			setTaxa(tree.getTaxa());
 
-	 	if (inProgress)
+	 	if (inProgress){
+			if (MesquiteTrunk.debugMode)
+				addToChain("TD-setTree HOLDING " + StringUtil.getDateTimeWithSeconds());
 	 		holdingTree = tree;
+	 	}
 	 	else {
 			this.tree = tree;
 			if (treeDrawing !=null) {
diff --git a/Source/mesquite/lib/TreeVector.java b/Source/mesquite/lib/TreeVector.java
index ea2853240..583cba97f 100644
--- a/Source/mesquite/lib/TreeVector.java
+++ b/Source/mesquite/lib/TreeVector.java
@@ -89,13 +89,19 @@ public void attachCloneToFile(MesquiteFile f, ElementManager manager){
 			
 		}
 	}
-	public boolean swapParts(int first, int second) {
+	/*public boolean swapPartsQ(int first, int second) {
 		
-		return swapParts(first, second, false);  //NOTE DEFAULT IS FALSE. The reason is to avoid time cost on multiple swaps
+		return swapParts(first, second, false, false);  //NOTE DEFAULT IS FALSE. The reason is to avoid time cost on multiple swaps
 	}
+	*/
 	public boolean swapParts(int first, int second, boolean resetNumbers) {
 		
-		boolean success = super.swapParts(first, second);
+		return swapParts(first, second, false, resetNumbers);  //NOTE DEFAULT IS FALSE. The reason is to avoid time cost on multiple swaps
+	}
+
+	public boolean swapParts(int first, int second, boolean notify, boolean resetNumbers) {
+		
+		boolean success = super.swapParts(first, second, notify);
 		if (resetNumbers)
 			resetAssignedNumbers();
 		return success;
diff --git a/Source/mesquite/lib/characters/CharSpecsSet.java b/Source/mesquite/lib/characters/CharSpecsSet.java
index b9a7c1b47..11425c879 100644
--- a/Source/mesquite/lib/characters/CharSpecsSet.java
+++ b/Source/mesquite/lib/characters/CharSpecsSet.java
@@ -34,7 +34,7 @@ public interface CharSpecsSet extends Listable, Identifiable {
 	public boolean moveParts(int first, int num, int justAfter);
 	/*.................................................................................................................*/
 	/*.................................................................................................................*/
-	public boolean swapParts(int first, int second);
+	public boolean swapParts(int first, int second, boolean notify);
 	
 	public CharacterData getCharacterData();
 }
diff --git a/Source/mesquite/lib/characters/CharacterData.java b/Source/mesquite/lib/characters/CharacterData.java
index 44901ba3d..b5f16b9ec 100644
--- a/Source/mesquite/lib/characters/CharacterData.java
+++ b/Source/mesquite/lib/characters/CharacterData.java
@@ -84,6 +84,7 @@ public abstract class CharacterData extends FileElement implements MesquiteListe
 	private Vector cellObjects; //Vector of arrays of objects (Object2DArray) that are attached to cells.  A courtesy to modules, so that they can attach and maintain info at the cells
 	private boolean[][] cellObjectsDisplay; //indicates whether there exist cell objects at a cell that need to be displayed in any way
 	private boolean[][] changedSinceSave; //records whether changed since last save.  
+	private boolean anyChangesSinceSave= false;
 	private int[] firstApplicable; //records the character number of the first non-applicable character.  
 	private int[] lastApplicable; //records the character number of the first non-applicable character.  
 
@@ -162,7 +163,7 @@ public CharacterData(CharMatrixManager matrixManager, int numTaxa, int numChars,
 		/* the following should probably be done only on demand (e.g., so that simulation matrices don't need to remake this)*/
 		characterNames = new String[numChars];
 		cellObjects = new Vector();
-		cellObjectsDisplay = new boolean[numChars][numTaxa];
+		cellObjectsDisplay = null; //make on demand;  new boolean[numChars][numTaxa];
 		changedSinceSave = new boolean[numChars][numTaxa];
 		firstApplicable = new int[numTaxa];
 		lastApplicable = new int[numTaxa];
@@ -189,6 +190,7 @@ public void disconnectListening(){
 	public void nullifyBooleanArrays () {
 		cellObjectsDisplay = null;
 		changedSinceSave = null;
+		anyChangesSinceSave = false;
 	}
 	/*.................................................................................................................*/
 	public boolean getCharNumChanging() {
@@ -792,8 +794,6 @@ else if (starting>=numChars)
 			newCharIDs[i + starting+num+1] = charIDs[starting + i+1];
 		charIDs = newCharIDs;
 
-
-
 		if (characterNames!=null){
 			characterNames = StringArray.addParts(characterNames, starting, num);
 		}
@@ -840,17 +840,18 @@ else if (starting>=numChars)
 		}
 		if (changedSinceSave!=null){
 			boolean[][] newCOD = new boolean[newNumChars][numTaxa];
-			for (int j = 0; j<numTaxa; j++){
-				for (int i=0; i<=starting; i++)
-					newCOD[i][j] = changedSinceSave[i][j];
-				for (int i=0; i<num; i++)
-					newCOD[starting + i + 1][j] = false;
-				for (int i=0; i<numChars-starting-1; i++) 
-					newCOD[i + starting+num+1][j] = changedSinceSave[starting + i+1][j];
+			if (anyChangesSinceSave){
+				for (int j = 0; j<numTaxa; j++){
+					for (int i=0; i<=starting; i++)
+						newCOD[i][j] = changedSinceSave[i][j];
+					//	for (int i=0; i<num; i++) default is false; don't need to set
+					//		newCOD[starting + i + 1][j] = false;
+					for (int i=0; i<numChars-starting-1; i++) 
+						newCOD[i + starting+num+1][j] = changedSinceSave[starting + i+1][j];
+				}
 			}
 			changedSinceSave = newCOD;
 		}
-
 		if (characterIllustrations!=null){
 			Image[] newCharacterIllustrations = new Image[newNumChars];
 			for (int i=0; i<=starting; i++) {
@@ -987,14 +988,15 @@ else if (starting>numChars)
 		}
 		if (changedSinceSave!=null){
 			boolean[][] newCOD = new boolean[newNumChars][numTaxa];
-			for (int j = 0; j<numTaxa; j++){
-				for (int i=0; i<starting; i++) {
-					newCOD[i][j] = changedSinceSave[i][j];
-				}
-				for (int i=starting+num; i<changedSinceSave.length; i++) {
-					newCOD[i -num][j] = changedSinceSave[i][j];
+			if (anyChangesSinceSave)
+				for (int j = 0; j<numTaxa; j++){
+					for (int i=0; i<starting; i++) {
+						newCOD[i][j] = changedSinceSave[i][j];
+					}
+					for (int i=starting+num; i<changedSinceSave.length; i++) {
+						newCOD[i -num][j] = changedSinceSave[i][j];
+					}
 				}
-			}
 			changedSinceSave = newCOD;
 		}
 
@@ -1068,7 +1070,8 @@ public boolean moveParts(int starting, int num, int justAfter){
 		notifyOfChangeLowLevel(MesquiteListener.PARTS_MOVED, starting, num, justAfter);  
 
 		Bits.moveColumns(cellObjectsDisplay, starting, num, justAfter);
-		Bits.moveColumns(changedSinceSave, starting, num, justAfter);
+		if (anyChangesSinceSave)
+			Bits.moveColumns(changedSinceSave, starting, num, justAfter);
 		calculateFirstLastApplicable();
 		MesquiteImage.moveParts( characterIllustrations, starting, num, justAfter); 
 		charIDs = LongArray.getMoveParts(charIDs, starting, num, justAfter);
@@ -1104,7 +1107,8 @@ public boolean swapCellMetadata(int first, int second){
 			}
 		}
 		Bits.swapColumns(cellObjectsDisplay,  first, second);
-		Bits.swapColumns(changedSinceSave,  first, second);
+		if (anyChangesSinceSave)
+			Bits.swapColumns(changedSinceSave,  first, second);
 
 		uncheckThread();
 		return true;
@@ -1123,7 +1127,8 @@ public boolean swapCellMetadata(int first, int second, int it){
 			}
 		}
 		Bits.swapCell(cellObjectsDisplay,  first, second, it);
-		Bits.swapCell(changedSinceSave,  first, second, it);
+		if (anyChangesSinceSave)
+			Bits.swapCell(changedSinceSave,  first, second, it);
 
 		uncheckThread();
 		return true;
@@ -1148,13 +1153,18 @@ public boolean swapCharacterMetadata(int first, int second){
 		calculateFirstLastApplicable();
 		MesquiteImage.swapParts( characterIllustrations,  first, second); 
 		nMove++;
-		boolean swapped =  super.swapParts( first, second);
+		boolean swapped =  super.swapParts( first, second, true);
 		uncheckThread();
 		return swapped;
 	}
 	/*-----------------------------------------------------------*/
 	/**Swaps characters first and second.*/
 	public boolean swapParts(int first, int second){
+		return swapParts(first, second, true);
+	}
+	/*-----------------------------------------------------------*/
+	/**Swaps characters first and second.*/
+	public boolean swapParts(int first, int second, boolean notify){
 		boolean meta = swapCellMetadata(first, second);
 		if (!meta)
 			return false;
@@ -1168,7 +1178,7 @@ public final void swapInLinked(int first, int second, boolean notify){
 		if (linkedDatas.size()>0){
 			for (int i=0; i<linkedDatas.size(); i++){
 				CharacterData d = (CharacterData)linkedDatas.elementAt(i);
-				d.swapParts(first, second);
+				d.swapParts(first, second, notify);
 				if (notify)
 					d.notifyListeners(this, new Notification(MesquiteListener.PARTS_MOVED));
 			}
@@ -1489,7 +1499,7 @@ public void equalizeCharacter(CharacterData oData, int oic, int ic){
 			characterNames[ic] = oData.characterNames[oic];
 			notifyOfChangeLowLevel(MesquiteListener.NAMES_CHANGED, ic, -1, 0);  
 		}
-		
+
 		for (int it = 0; it<getNumTaxa(); it++){
 			incrementSuppressHistoryStamp();
 			int oit = oData.getTaxa().findEquivalentTaxon(getTaxa(), it);
@@ -1911,15 +1921,18 @@ public void tradeStatesBetweenCharacters(int ic, int ic2, int it, boolean adjust
 				objArray.setValue(ic2, it, ob);
 			}
 		}
-		boolean t = cellObjectsDisplay[ic][it];
-		cellObjectsDisplay[ic][it] = cellObjectsDisplay[ic2][it];
-		cellObjectsDisplay[ic2][it] = t;
+		if (cellObjectsDisplay != null){
+			boolean t = cellObjectsDisplay[ic][it];
+			cellObjectsDisplay[ic][it] = cellObjectsDisplay[ic2][it];
+			cellObjectsDisplay[ic2][it] = t;
+		}
 		if (adjustCellLinked){
 			for (int i=0; i<linkedDatas.size(); i++){
 				CharacterData d= (CharacterData)linkedDatas.elementAt(i);
 				d.tradeStatesBetweenCharacters(ic,ic2,it,false);
 			}
 		}
+
 	}
 	/** trades the states of character ic between taxa it and it2.  Used for reshuffling (for example).*/
 	public void tradeStatesBetweenTaxa(int ic, int it, int it2){
@@ -1940,9 +1953,11 @@ public void tradeStatesBetweenTaxa(int ic, int it, int it2){
 				objArray.setValue(ic, it2, ob);
 			}
 		}
-		boolean t = cellObjectsDisplay[ic][it];
-		cellObjectsDisplay[ic][it] = cellObjectsDisplay[ic][it2];
-		cellObjectsDisplay[ic][it2] = t;
+		if (cellObjectsDisplay != null){
+			boolean t = cellObjectsDisplay[ic][it];
+			cellObjectsDisplay[ic][it] = cellObjectsDisplay[ic][it2];
+			cellObjectsDisplay[ic][it2] = t;
+		}
 	}
 
 	/** returns whether the matrix would prefer to have columns sized individually in editors.  Default is true.*/
@@ -2728,6 +2743,7 @@ public void resetChangedSinceSave() {
 				}
 		watchForChange = true;	
 		checksumValid = false;
+		anyChangesSinceSave = false;
 		if (c)
 			notifyListeners(this, new Notification(MesquiteListener.ANNOTATION_CHANGED));
 	}
@@ -2758,8 +2774,12 @@ public void setCellObjectDisplay(int ic, int it) {
 		if (ic<0 || ic>=numChars || it<0 || it>=numTaxa) {
 			return;
 		}
-		else if (cellObjectsDisplay!=null && !(ic<0 || ic>=cellObjectsDisplay.length || it<0 || cellObjectsDisplay[ic]==null || it>=cellObjectsDisplay[ic].length)){
-			cellObjectsDisplay[ic][it] = true;
+		else {
+			
+			if (cellObjectsDisplay==null)
+				cellObjectsDisplay = new boolean[numChars][numTaxa];
+			if ( !(ic<0 || ic>=cellObjectsDisplay.length || it<0 || cellObjectsDisplay[ic]==null || it>=cellObjectsDisplay[ic].length))
+				cellObjectsDisplay[ic][it] = true;
 		}
 	}
 	/*.................................................................................................................*/
@@ -2977,8 +2997,10 @@ public void stampHistoryChange(int ic, int it) {
 			return;
 		}
 		else {
-			if (changedSinceSave!=null && !(ic<0 || ic>=changedSinceSave.length || it<0 || changedSinceSave[ic]==null || it>=changedSinceSave[ic].length))
+			if (changedSinceSave!=null && !(ic<0 || ic>=changedSinceSave.length || it<0 || changedSinceSave[ic]==null || it>=changedSinceSave[ic].length)){
 				changedSinceSave[ic][it] = true;
+				anyChangesSinceSave = true;
+			}
 			notifyOfChangeLowLevel(MesquiteListener.DATA_CHANGED, ic, it, 0);  
 			checksumValid = false;
 			//if (watchForChange)
@@ -3026,8 +3048,10 @@ public void stampHistoryChange(int ic, int it) {
 	public void stampHistoryChange() {
 		if (changedSinceSave!=null)
 			for (int ic = 0; ic<getNumChars(); ic++)
-				for (int it = 0; it<numTaxa; it++)
+				for (int it = 0; it<numTaxa; it++){
 					changedSinceSave[ic][it] = true;
+					anyChangesSinceSave = true;
+				}
 	}
 
 	/*.................................................................................................................*/
@@ -3700,7 +3724,6 @@ public boolean concatenate(CharacterData oData, boolean addTaxaIfNew, boolean co
 		}
 
 		addInLinked(getNumChars()+1, oData.getNumChars(), true);
-
 		CharacterState cs = null;
 		int count=0;
 		for (int ic = 0; ic<oData.getNumChars(); ic++){
@@ -3710,7 +3733,6 @@ public boolean concatenate(CharacterData oData, boolean addTaxaIfNew, boolean co
 				count++;
 			}
 		}
-
 		if (oPartition != null && adjustGroupLabels)
 			adjustGroupLabels(oData.getName(), origNumChars, getNumChars()-1, true, prefixGroupNamesIfAlreadyAssigned, module);  //there exists a partition in the incoming, so just redo the names for the groups there.
 
@@ -3970,7 +3992,7 @@ public boolean[] mergeTaxa(int sinkTaxon, boolean[]taxaToMerge, boolean mergeMul
 					//in this case tInfo brought in from merging.  This isn't ideal, as should fuse tInfo if both have data
 					Associable a = getTaxaInfo(false);
 					if (a != null)
-						a.swapParts(sinkTaxon, it);
+						a.swapParts(sinkTaxon, it, true);
 				}
 				mA[it] = ma;   
 				mergedAssigned = mergedAssigned | ma;
@@ -3990,7 +4012,7 @@ public boolean[] mergeTaxa(int sinkTaxon, boolean[]taxaToMerge, boolean mergeMul
 	public boolean[] mergeTaxa(int sinkTaxon, boolean[]taxaToMerge) {
 		return mergeTaxa(sinkTaxon, taxaToMerge, false);
 	}
-	
+
 	/*..........................................CharacterData.....................................*/
 	/**Gets the CharacterData object for an MCharactersDistribution.  It first checks to see if the CharacterData object
 	 * already exists, and if so, returns it; otherwise, it created one.  */
diff --git a/Source/mesquite/lib/characters/CharacterState.java b/Source/mesquite/lib/characters/CharacterState.java
index d9bab314b..053de6b10 100644
--- a/Source/mesquite/lib/characters/CharacterState.java
+++ b/Source/mesquite/lib/characters/CharacterState.java
@@ -92,7 +92,9 @@ public abstract class CharacterState {
 	/** returns whether value is combinable (i.e. a valid assigned state) or not.*/
 	public abstract boolean isCombinable();
 	/** returns whether the contents of the character states could be identical, given ambiguity*/
-	public abstract boolean couldBeEqual(CharacterState s);
+	public boolean couldBeEqual(CharacterState s){ 
+		return true;
+	}
 	/** returns whether the contents of the character states are identical*/
 	public abstract boolean equals(CharacterState s);
 	/** returns whether the contents of the character states are identical, allowing some to be missing if allowMissing is true*/
diff --git a/Source/mesquite/lib/characters/CodonPositionsSet.java b/Source/mesquite/lib/characters/CodonPositionsSet.java
index f09f265ab..5cfdaccc5 100644
--- a/Source/mesquite/lib/characters/CodonPositionsSet.java
+++ b/Source/mesquite/lib/characters/CodonPositionsSet.java
@@ -54,6 +54,7 @@ public boolean addParts(int starting, int num){
 		return success;
 	}
   	
+  	/** **/
 	int endSequenceByThree(int targetPos, int numChars, int ic, int mainCount, boolean[] include, MesquiteInteger charNumberOfLastThird){
 		int unassignedPosition=4;
 		int previousThird = mainCount; 
@@ -61,7 +62,7 @@ int endSequenceByThree(int targetPos, int numChars, int ic, int mainCount, boole
 		int count=mainCount;
 		int ik=0;
 		for (ik = ic+1; ik< numChars; ik++){
-			if (include==null || ik>=include.length || include[ik]){
+			if (include==null || ik>=include.length || include[ik]){// only pay attention to included characters if the boolean array "include" is present
 				count++;
 				int thisPos = getInt(ik);
 				if (thisPos == targetPos || (thisPos==MesquiteInteger.unassigned && (targetPos==unassignedPosition))) {
@@ -104,7 +105,7 @@ public String getListOfMatches(int targetPos, int offset, boolean[] include, boo
 				count++;
 				int thisPos = getInt(ic);
 				if (thisPos == targetPos || (thisPos==MesquiteInteger.unassigned && (targetPos==unassignedPosition))) {
-					if (continuing == 0) { 
+					if (continuing == 0) {
 						//first, check to see if there is a series of thirds....
 						int lastThird = endSequenceByThree(targetPos, getNumberOfParts(), ic, count, include, charNumberOfLastThird);
 						//if so, then go the series of thirds 
@@ -115,6 +116,8 @@ public String getListOfMatches(int targetPos, int offset, boolean[] include, boo
 							}
 
 							list += " " + CharacterStates.toExternal(count+offset) + "-" +  CharacterStates.toExternal(lastThird+offset) + "\\3";
+							if (writeCommas)
+								writeSeparator=true;
 							ic = charNumberOfLastThird.getValue();
 							count = lastThird;
 						
@@ -141,6 +144,8 @@ else if (continuing>0) {   // we are in a contiguous stretch of the same thing
 							writeSeparator=false;
 						}
 						list += " " + CharacterStates.toExternal(count-1+offset);
+						if (writeCommas)
+							writeSeparator=true;
 						lastWritten = count-1;
 					}
 					else {
diff --git a/Source/mesquite/lib/duties/CharMatrixManager.java b/Source/mesquite/lib/duties/CharMatrixManager.java
index 914243ba9..e20c257c7 100644
--- a/Source/mesquite/lib/duties/CharMatrixManager.java
+++ b/Source/mesquite/lib/duties/CharMatrixManager.java
@@ -262,7 +262,7 @@ else if (nameTaxa && it<taxa.getNumTaxa())
 				MesquiteTrunk.errorReportedDuringRun = true;
 			}
 			if (warnChimera>=0){
-				discreetAlert("WARNING: The merging process resulted in INCORRECT assignments of states for taxon " + (warnChimera+1) + " (" + taxa.getTaxonName(warnChimera) + ").  The problem may have affected other taxa as well.  It is recommended that you DO NOT SAVE THE FILE and instead merge again so as to prevent this.  To prevent this, ensure that the incoming (merging) data matrix is NOT INTERLEAVED.  Interleaving the matrix presents special problems in merging.");
+				discreetAlert("WARNING: The merging process resulted in INCORRECT assignments of states for taxon " + (warnChimera+1) + " (" + taxa.getTaxonName(warnChimera) + ") in matrix " + data.getName() + ".  The problem may have affected other taxa as well.  It is recommended that you DO NOT SAVE THE FILE and instead merge again so as to prevent this.  To prevent this, ensure that the incoming (merging) data matrix is NOT INTERLEAVED.  Interleaving the matrix presents special problems in merging.");
 				MesquiteTrunk.errorReportedDuringRun = true;
 			}
 			if (toDelete){
diff --git a/Source/mesquite/lib/duties/DataAlterer.java b/Source/mesquite/lib/duties/DataAlterer.java
index 6c5d55b7e..081d83d24 100644
--- a/Source/mesquite/lib/duties/DataAlterer.java
+++ b/Source/mesquite/lib/duties/DataAlterer.java
@@ -36,7 +36,10 @@ public String getDutyName() {
  		return "Data Alterer";
    	}
    	
-   	public long getNumCellsAltered(){
+ 	 public String[] getDefaultModule() {
+	 	return new String[] {"#MultipleAlignService"};
+	 }
+  	public long getNumCellsAltered(){
    		return numCellsAltered;
    	}
    	/** if returns true, then requests to remain on even after operateData is called.  Default is false*/
diff --git a/Source/mesquite/lib/duties/FileCoordinator.java b/Source/mesquite/lib/duties/FileCoordinator.java
index 521952b6e..0502a1773 100644
--- a/Source/mesquite/lib/duties/FileCoordinator.java
+++ b/Source/mesquite/lib/duties/FileCoordinator.java
@@ -26,6 +26,7 @@
 public abstract class FileCoordinator extends MesquiteModule {
 	public static boolean maxLinesOfAnyElementInPanelQueried = false; // has this been set by the user?
 	public static int maxLinesOfAnyElementInPanel = 50; //starts here; if exceeded and hasn't been previously set, then asks user for value. Preferences saved by mesquite.minimal.Defaults
+	public static int maxLinesOfMatricesTreeBlocksSeparateInPanel = 16; //starts here; if exceeded and hasn't been previously set, then asks user for value. Preferences saved by mesquite.minimal.Defaults
 	
 	public boolean getSearchableAsModule(){
 		return false;
diff --git a/Source/mesquite/lib/duties/FileInterpreter.java b/Source/mesquite/lib/duties/FileInterpreter.java
index 089b6522a..95943900e 100644
--- a/Source/mesquite/lib/duties/FileInterpreter.java
+++ b/Source/mesquite/lib/duties/FileInterpreter.java
@@ -32,6 +32,7 @@ public abstract class FileInterpreter extends MesquiteModule  {
 	public static final int WINDOWSDELIMITER=2;
 	public static final int UNIXDELIMITER=3;
 	public int lineDelimiter = CURRENTDELIMITER;
+	public boolean writeCharLabels = true;
 	public boolean writeOnlySelectedData = false;
 	public boolean writeOnlyIncludedData = true;
 	public boolean writeOnlySelectedTaxa = false;
diff --git a/Source/mesquite/lib/duties/FileProcessor.java b/Source/mesquite/lib/duties/FileProcessor.java
index ddf333fe8..51090e541 100644
--- a/Source/mesquite/lib/duties/FileProcessor.java
+++ b/Source/mesquite/lib/duties/FileProcessor.java
@@ -29,7 +29,10 @@ public abstract class FileProcessor extends MesquiteModule  {
    	 public Class getDutyClass() {
    	 	return FileProcessor.class;
    	 }
- 	public String getDutyName() {
+  	 public String[] getDefaultModule() {
+ 	 	return new String[] {"#AlterAllMatrices", "#CompileProcessedMatrices", "#FAFillTreeBlock", "#CopyTreesToNexusBlock", "#CopyTreesToSimpleFile"};
+ 	 }
+	public String getDutyName() {
  		return "File Processor";
    	}
    	
@@ -41,11 +44,21 @@ public boolean pleaseLeaveMeOn(){
    		return false;
    	}
 	/*.................................................................................................................*/
+   	/** Called before processing a series of files.*/
+   	public  boolean beforeProcessingSeriesOfFiles(){
+   		return true;
+   	}
+	/*.................................................................................................................*/
    	/** Called to process file. Override this or the next*/
    	public  boolean processFile(MesquiteFile file){
    		return true;
    	}
   	
+	/*.................................................................................................................*/
+   	/** Called after processing a series of files.*/
+   	public  boolean afterProcessingSeriesOfFiles(){
+   		return true;
+   	}
 	/*.................................................................................................................*/
    	/** If a processor wants, it can request to have the file sequestered once all processing is done*/
    	public  boolean pleaseSequester(){
diff --git a/Source/mesquite/lib/duties/NodeLocsVH.java b/Source/mesquite/lib/duties/NodeLocsVH.java
index e069a5186..c690773f2 100644
--- a/Source/mesquite/lib/duties/NodeLocsVH.java
+++ b/Source/mesquite/lib/duties/NodeLocsVH.java
@@ -23,7 +23,7 @@
 Example Module: NodeLocsStandard*/
 
 public abstract class NodeLocsVH extends NodeLocs  {
-	public static int defaultOrientation = TreeDisplay.UP;
+	public static int defaultOrientation = TreeDisplay.RIGHT;
  	public String getDutyName() {
  		return "Node Location (Vert/Horiz)";
    	 }
@@ -32,7 +32,7 @@ public Class getDutyClass() {
    	 }
 	/** gets the module's default tree display orientation.*/
    	public int getDefaultOrientation(){
-   		return TreeDisplay.UP;
+   		return TreeDisplay.RIGHT;
    	}
    	
 }
diff --git a/Source/mesquite/lib/table/MesquiteTable.java b/Source/mesquite/lib/table/MesquiteTable.java
index b36d76823..0f440b342 100644
--- a/Source/mesquite/lib/table/MesquiteTable.java
+++ b/Source/mesquite/lib/table/MesquiteTable.java
@@ -4928,7 +4928,11 @@ public boolean isCellSelectedAnyWay(int column, int row) {
 			return  isRowSelected(row) || isColumnSelected(column) || (cellsSelected[0].isBitOn(row * numColumnsTotal + column)) ;
 		return false;
 	}
-
+	public void synchronizeRowSelection(){
+		if (rowAssociable != null){
+			synchronizeRowSelection(rowAssociable);
+		}
+	}
 	public void synchronizeRowSelection(Associable a) {
 		if (a == null)
 			return;
@@ -4944,6 +4948,11 @@ public void synchronizeRowSelection(Associable a) {
 			}
 	}
 
+	public void synchronizeColumnSelection(){
+		if (columnAssociable != null){
+			synchronizeColumnSelection(columnAssociable);
+		}
+	}
 	public void synchronizeColumnSelection(Associable a) {
 		if (a == null)
 			return;
diff --git a/Source/mesquite/lib/table/RowNamesPanel.java b/Source/mesquite/lib/table/RowNamesPanel.java
index c49cd4908..8c58d29ce 100644
--- a/Source/mesquite/lib/table/RowNamesPanel.java
+++ b/Source/mesquite/lib/table/RowNamesPanel.java
@@ -209,7 +209,7 @@ public void paint(Graphics g) {
 			height = resetHeight;
 			Shape clip = g.getClip();
 
-			for (int r=table.firstRowVisible; (r<table.numRowsTotal) && (lineY<height); r++) {
+			for (int r=table.firstRowVisible; (r<=table.lastRowVisible && r<table.numRowsTotal) && (lineY<height); r++) {
 				redrawName(g, r);
 			}
 
diff --git a/Source/mesquite/lists/CharGroupList/CharGroupList.java b/Source/mesquite/lists/CharGroupList/CharGroupList.java
index 346751c89..b9a92afc8 100644
--- a/Source/mesquite/lists/CharGroupList/CharGroupList.java
+++ b/Source/mesquite/lists/CharGroupList/CharGroupList.java
@@ -256,9 +256,10 @@ public void setRowName(int row, String name){
 	}
 	public String getRowName(int row){
 		if (groups!=null){
-			if (row<0 && row >= groups.size())
+			if (row<0 || row >= groups.size())
 				return null;
-			return ((Listable)groups.elementAt(row)).getName();
+			Listable g = (Listable)groups.elementAt(row);
+			return g.getName();
 		}
 		else
 			return null;
diff --git a/Source/mesquite/lists/CharListPartition/CharListPartition.java b/Source/mesquite/lists/CharListPartition/CharListPartition.java
index c1ce5a868..aa087f5b4 100644
--- a/Source/mesquite/lists/CharListPartition/CharListPartition.java
+++ b/Source/mesquite/lists/CharListPartition/CharListPartition.java
@@ -19,6 +19,7 @@
 import java.util.*;
 import java.awt.*;
 
+import mesquite.categ.lib.DNAData;
 import mesquite.lib.*;
 import mesquite.lib.characters.*;
 import mesquite.lib.duties.*;
@@ -37,7 +38,7 @@ public String getExplanation() {
 	CharacterData data=null;
 	MesquiteTable table=null;
 	MesquiteSubmenuSpec mss, mEGC, mDGC, mEGN;
-	MesquiteMenuItemSpec mScs, mStc, mRssc, mLine, nNG, mLine2, mss2;
+	MesquiteMenuItemSpec mScs, mStc, mRssc, mLine, nNG, mLine2, mss2, msRCP;
 	CharactersGroupVector groups;
 	/*.................................................................................................................*/
 	public boolean startJob(String arguments, Object condition, boolean hiredByName) {
@@ -92,6 +93,45 @@ private void setPartition(CharactersGroup group, String arguments){
 			}
 		}
 	}
+	private void refineByCodonPosition(){
+		if (table !=null && data!=null) {
+			boolean changed=false;
+			CodonPositionsSet codons = (CodonPositionsSet) data.getCurrentSpecsSet(CodonPositionsSet.class);
+			CharacterPartition partition = (CharacterPartition) data.getCurrentSpecsSet(CharacterPartition.class);
+			if (codons == null || partition == null)
+				return;
+			if (employer!=null && employer instanceof ListModule) {
+				int c = ((ListModule)employer).getMyColumn(this);
+				for (int i=0; i<data.getNumChars(); i++) {
+					if (table.isCellSelectedAnyWay(c, i)) {
+						if (codons.getInt(i)>0 && codons.getInt(i)<=3 ){
+							CharactersGroup currentGroup = (CharactersGroup)partition.getProperty(i);
+							String newName = currentGroup.getName() + "_" + codons.toString(i);
+							CharactersGroup newGroup = (CharactersGroup)groups.elementWithName(newName);
+							if (newGroup == null){
+								newGroup = new CharactersGroup();
+								newGroup.setName(newName);
+								newGroup.setColor(currentGroup.getColor());
+								newGroup.setSymbol(currentGroup.getSymbol());
+								groups.addElement(newGroup, true);
+							}
+							partition.setProperty(newGroup, i);
+							if (!changed)
+								outputInvalid();
+							changed = true;
+						}
+					}
+				}
+			}
+
+			if (changed)
+				data.notifyListeners(this, new Notification(MesquiteListener.NAMES_CHANGED)); //TODO: bogus! should notify via specs not data???
+			outputInvalid();
+			parametersChanged();
+
+
+		}
+	}
 	private void removePartition(){
 		if (table !=null && data!=null) {
 			boolean changed=false;
@@ -209,6 +249,9 @@ else if (checker.compare(this.getClass(), "Loads the stored character partition
 		else if (checker.compare(this.getClass(), "Removes the group designation from the selected characters", null, commandName, "removeGroup")) {
 			removePartition();
 		}
+		else if (checker.compare(this.getClass(), "Refines current groups by intersecting them with codon positions", null, commandName, "refineByCodonPosition")) {
+			refineByCodonPosition();
+		}
 		else
 			return  super.doCommand(commandName, arguments, checker);
 		return null;
@@ -233,6 +276,10 @@ public void setTableAndData(MesquiteTable table, CharacterData data){
 		deleteMenuItem(nNG);
 		mss = addSubmenu(null, "Set Group", makeCommand("setPartition", this));
 		mss.setList((StringLister)getProject().getFileElement(CharactersGroupVector.class, 0));
+		if (data != null && data instanceof DNAData)
+			msRCP =	 addMenuItem("Refine Groups by Codon Position", makeCommand("refineByCodonPosition", this));
+
+			
 		mss2 = addMenuItem("Remove Group Designation", makeCommand("removeGroup", this));
 		mLine2 = addMenuSeparator();
 		nNG = addMenuItem("New Group...", makeCommand("newGroup",  this));
diff --git a/Source/mesquite/lists/DatasetList/DatasetList.java b/Source/mesquite/lists/DatasetList/DatasetList.java
index 8cabaee46..06e489ec5 100644
--- a/Source/mesquite/lists/DatasetList/DatasetList.java
+++ b/Source/mesquite/lists/DatasetList/DatasetList.java
@@ -50,6 +50,14 @@ public boolean showing(Object obj){
 	public boolean resetMenusOnNameChange(){
 		return true;
 	}
+	public boolean rowsShowable(){
+		return true;
+	}
+	public void showItemAtRow(int row){
+		CharacterData data = (CharacterData)datas.elementAt(row);
+		data.showMe();
+		
+	}
 	public void showListWindow(Object obj){
 		CharMatricesListWindow charMatricesListWindow = new CharMatricesListWindow(this);
 		charMatricesListWindow.setDatas(datas);
@@ -124,7 +132,6 @@ public boolean deleteRow(int row, boolean notify){
 		if (row<0 || row>= getNumberOfRows())
 			return false;
 		CharacterData data = getProject().getCharacterMatrixDoomedOrNot(row);
-		getProject().removeFileElement(data);//must remove first, before disposing
 		data.dispose();
 		return true;
 	}
diff --git a/Source/mesquite/lists/DatasetsListConcatenate/DatasetsListConcatenate.java b/Source/mesquite/lists/DatasetsListConcatenate/DatasetsListConcatenate.java
index 07a5533b2..2ec9690cc 100644
--- a/Source/mesquite/lists/DatasetsListConcatenate/DatasetsListConcatenate.java
+++ b/Source/mesquite/lists/DatasetsListConcatenate/DatasetsListConcatenate.java
@@ -133,20 +133,19 @@ public boolean operateOnDatas(ListableVector datas, MesquiteTable table){
 
 				starter.addToFile(getProject().getHomeFile(), getProject(),  findElementManager(CharacterData.class));  
 			}
-
 			boolean success = starter.concatenate(data, false, concatExcludedCharacters, true, prefixGroupLabelNames, false, false);
 			if (success){
 				count++;
 				if (count > 1)
 					name = name + "+";
 				name = name + "(" + data.getName() + ")";
-				if (removeConcatenated)
+				if (removeConcatenated){
 						data.deleteMe(false);
+				}
 			}
 			else 
 				countFailed++;
 
-
 		}
 		if (starter != null)
 			starter.setName(name);
diff --git a/Source/mesquite/lists/ModelsList/ModelsList.java b/Source/mesquite/lists/ModelsList/ModelsList.java
index 275dc7c26..edfc46d18 100644
--- a/Source/mesquite/lists/ModelsList/ModelsList.java
+++ b/Source/mesquite/lists/ModelsList/ModelsList.java
@@ -112,7 +112,7 @@ public boolean deleteRow(int row, boolean notify){
 				return false;
 			}
 			else {
-				getProject().removeFileElement(model);//must remove first, before disposing
+				getProject().removeFileElement(model, notify);//must remove first, before disposing
 				model.dispose();
 				return true;
 			}
@@ -238,7 +238,7 @@ public void setRowName(int row, String name){
 	}
 	public String getRowName(int row){
 		if (models!=null){
-			if (row<0 && row >= models.size())
+			if (row<0 || row >= models.size())
 				return null;
 			return ((Listable)models.elementAt(row)).getName();
 		}
diff --git a/Source/mesquite/lists/NumForCharMatrixList/NumForCharMatrixList.java b/Source/mesquite/lists/NumForCharMatrixList/NumForCharMatrixList.java
index f6e5d738f..cd90181a5 100644
--- a/Source/mesquite/lists/NumForCharMatrixList/NumForCharMatrixList.java
+++ b/Source/mesquite/lists/NumForCharMatrixList/NumForCharMatrixList.java
@@ -23,7 +23,7 @@
 import mesquite.lib.table.*;
 
 /* ======================================================================== */
-public class NumForCharMatrixList extends DataSetsListAssistant  {
+public class NumForCharMatrixList extends DataSetsListAssistant implements MesquiteListener  {
 	/*.................................................................................................................*/
 	public String getName() {
 		return "Number for Matrix (in List of Character Matrices window)";
@@ -39,6 +39,8 @@ public String getExplanation() {
 		"You can select a value to show in the Number For Character Matrices submenu of the Columns menu of the List of Character Matrices Window. ");
 	}
 	NumberForMatrix numberTask;
+	MesquiteBoolean shadeCells = new MesquiteBoolean(false);
+	MesquiteTable table;
 	/*.................................................................................................................*/
 	public boolean startJob(String arguments, Object condition, boolean hiredByName) {
 		if (arguments !=null) {
@@ -52,6 +54,9 @@ public boolean startJob(String arguments, Object condition, boolean hiredByName)
 		if (numberTask==null) {
 			return sorry("Number for character matrix (for list) can't start because the no calculating module was successfully hired");
 		}
+		shadeCells.setValue(false);
+		addCheckMenuItem(null, "Color Cells", makeCommand("toggleShadeCells",  this), shadeCells);
+		addMenuItem(null, "Select based on value...", makeCommand("selectBasedOnValue",  this));
 		return true;
 	}
 	/** Returns whether or not it's appropriate for an employer to hire more than one instance of this module.  
@@ -69,12 +74,14 @@ public void setTableAndObject(MesquiteTable table, Object obj){
 		if (obj instanceof ListableVector)
 			this.datas = (ListableVector)obj;
 		datas.addListener(this);
+		this.table = table;
 		doCalcs();
 	}
 	/*.................................................................................................................*/
 	/** passes which object is being disposed (from MesquiteListener interface)*/
 	public void disposing(Object obj){
-		//TODO: respond
+		if (obj == datas)
+			datas=null;
 	}
 	/*.................................................................................................................*/
 	/** passes which object is being disposed (from MesquiteListener interface)*/
@@ -82,7 +89,8 @@ public boolean okToDispose(Object obj, int queryUser){
 		return true;  //TODO: respond
 	}
 	public void changed(Object caller, Object obj, Notification notification){
-		if (Notification.appearsCosmetic(notification))
+		// below should be appearsCosmeticOrSelection if matrix initiating 
+		if (Notification.appearsCosmeticOrSelection(notification))
 			return;
 		if (notification.getCode()!=MesquiteListener.LOCK_CHANGED)
 			doCalcs();
@@ -96,17 +104,96 @@ public Class getHireSubchoice(){
 	public Snapshot getSnapshot(MesquiteFile file) { 
 		Snapshot temp = new Snapshot();
 		temp.addLine("setValueTask ", numberTask); 
+		temp.addLine("toggleShadeCells " + shadeCells.toOffOnString());
 		return temp;
 	}
 	/*.................................................................................................................*/
+	public boolean querySelectBounds(MesquiteNumber lessThan, MesquiteNumber moreThan) {
+		if (lessThan==null || moreThan==null || numberTask==null)
+			return false;
+		MesquiteInteger buttonPressed = new MesquiteInteger(1);
+		ExtensibleDialog dialog = new ExtensibleDialog(containerOfModule(), "Select based upon value",buttonPressed); 
+
+		dialog.addLargeOrSmallTextLabel("Select based upon value of " + numberTask.getNameOfValueCalculated());
+
+		SingleLineTextField moreThanField = dialog.addTextField("Select values greater than or equal to ","",20);
+		SingleLineTextField lessThanField = dialog.addTextField("Select values less than or equal to ","",20);
+
+
+		dialog.completeAndShowDialog(true);
+
+		if (buttonPressed.getValue()==0)  {
+			String s = moreThanField.getText();
+			moreThan.setValue(s);
+			s = lessThanField.getText();
+			lessThan.setValue(s);
+		}
+		dialog.dispose();
+		return (buttonPressed.getValue()==0);
+	}
+	/*.................................................................................................................*/
+	void selectBasedOnValue() {
+		if (MesquiteThread.isScripting())
+			return;
+		if (table==null || datas==null || na==null)
+			return;
+		MesquiteNumber lessThan = new MesquiteNumber();
+		MesquiteNumber moreThan = new MesquiteNumber();
+		if (!querySelectBounds(lessThan, moreThan))
+			return;
+		if (!lessThan.isCombinable() && ! moreThan.isCombinable())
+			return;
+		MesquiteNumber value = new MesquiteNumber();
+		for (int i=0; i<datas.getNumberOfParts(); i++) {
+			na.placeValue(i, value);
+
+			if (lessThan.isCombinable() && moreThan.isCombinable()) {
+				if ((lessThan.isMoreThan(value)|| lessThan.equals(value)) &&  (moreThan.isLessThan(value) ||  moreThan.equals(value))) {
+					table.selectRow(i);
+					datas.setSelected(i, true);
+					table.redrawFullRow(i);
+				}
+			} else if (lessThan.isCombinable() && (lessThan.isMoreThan(value)|| lessThan.equals(value))) {
+				table.selectRow(i);
+				datas.setSelected(i, true);
+				table.redrawFullRow(i);
+			} else if (moreThan.isCombinable() && (moreThan.isLessThan(value) ||  moreThan.equals(value))) {
+				table.selectRow(i);
+				datas.setSelected(i, true);
+				table.redrawFullRow(i);
+			}
+		}
+		
+		datas.notifyListeners(this, new Notification(MesquiteListener.SELECTION_CHANGED));
+
+	}
+	/*.................................................................................................................*/
 	public Object doCommand(String commandName, String arguments, CommandChecker checker) {
 		if (checker.compare(this.getClass(), "Sets module that calculates a number for a character matrix", "[name of module]", commandName, "setValueTask")) {
 			NumberForMatrix temp= (NumberForMatrix)hireNamedEmployee(NumberForMatrix.class, arguments);
+			Class prev = null;
+			if (numberTask != null)
+				prev = numberTask.getClass();
 			if (temp!=null) {
 				numberTask = temp;
+				if (prev != numberTask.getClass()){
+					doCalcs();
+					outputInvalid();
+				}
 				return temp;
 			}
 		}
+		else if (checker.compare(this.getClass(), "Sets whether or not to color cells", "[on or off]", commandName, "toggleShadeCells")) {
+			boolean current = shadeCells.getValue();
+			shadeCells.toggleValue(parser.getFirstToken(arguments));
+			if (current!=shadeCells.getValue()) {
+				outputInvalid();
+				parametersChanged();
+			}
+		}
+		else if (checker.compare(this.getClass(), "Selects list rows based on value of this column", null, commandName, "selectBasedOnValue")) {
+			selectBasedOnValue();
+		}
 		else
 			return  super.doCommand(commandName, arguments, checker);
 		return null;
@@ -116,6 +203,15 @@ public String getTitle() {
 			return "";
 		return numberTask.getVeryShortName();
 	}
+	/** Gets background color for cell for row ic.  Override it if you want to change the color from the default. */
+	public Color getBackgroundColorOfCell(int ic, boolean selected){
+		if (!shadeCells.getValue())
+			return null;
+		if (min.isCombinable() && max.isCombinable() && na != null && na.isCombinable(ic)){
+			return MesquiteColorTable.getGreenScale(na.getDouble(ic), min.getDoubleValue(), max.getDoubleValue(), false);
+		}
+		return null;
+	}
 	/*.................................................................................................................*/
 	public void employeeParametersChanged(MesquiteModule employee, MesquiteModule source, Notification notification) {
 		if (Notification.appearsCosmetic(notification) || (notification!=null && notification.getCode()==MesquiteListener.LOCK_CHANGED)) 
@@ -126,6 +222,8 @@ public void employeeParametersChanged(MesquiteModule employee, MesquiteModule so
 	/*.................................................................................................................*/
 	NumberArray na = new NumberArray(0);
 	StringArray explArray = new StringArray(0);
+	MesquiteNumber min = new MesquiteNumber();
+	MesquiteNumber max = new MesquiteNumber();
 	/*.................................................................................................................*/
 	public void doCalcs(){
 		if (numberTask==null || datas == null)
@@ -135,6 +233,7 @@ public void doCalcs(){
 		explArray.resetSize(numBlocks);
 		MesquiteString expl = new MesquiteString();
 		na.resetSize(numBlocks);
+		na.deassignArrayToInteger();
 		MesquiteNumber mn = new MesquiteNumber();
 		for (int ic=0; ic<numBlocks; ic++) {
 			CharacterData data = (CharacterData)datas.elementAt(ic);
@@ -143,6 +242,8 @@ public void doCalcs(){
 			na.setValue(ic, mn);
 			explArray.setValue(ic, expl.getValue());
 		}
+		na.placeMinimumValue(min);
+		na.placeMaximumValue(max);
 	}
 	public String getExplanationForRow(int ic){
 		if (explArray == null || explArray.getSize() <= ic)
diff --git a/Source/mesquite/lists/NumForTreeblockList/NumForTreeblockList.java b/Source/mesquite/lists/NumForTreeblockList/NumForTreeblockList.java
index f7e2a5a17..8b5e2a2b7 100644
--- a/Source/mesquite/lists/NumForTreeblockList/NumForTreeblockList.java
+++ b/Source/mesquite/lists/NumForTreeblockList/NumForTreeblockList.java
@@ -102,8 +102,15 @@ public Snapshot getSnapshot(MesquiteFile file) {
 	public Object doCommand(String commandName, String arguments, CommandChecker checker) {
 		if (checker.compare(this.getClass(), "Sets module that calculates a number for a block of trees", "[name of module]", commandName, "setValueTask")) {
 			NumberForTreeBlock temp= (NumberForTreeBlock)hireNamedEmployee(NumberForTreeBlock.class, arguments);
+			Class prev = null;
+			if (numberTask != null)
+				prev = numberTask.getClass();
 			if (temp!=null) {
 				numberTask = temp;
+				if (prev != numberTask.getClass()){
+					doCalcs();
+					outputInvalid();
+				}
 				return temp;
 			}
 		}
diff --git a/Source/mesquite/lists/TaxablockList/TaxablockList.java b/Source/mesquite/lists/TaxablockList/TaxablockList.java
index ee2227f1c..e209ce2a0 100644
--- a/Source/mesquite/lists/TaxablockList/TaxablockList.java
+++ b/Source/mesquite/lists/TaxablockList/TaxablockList.java
@@ -121,7 +121,7 @@ public boolean deleteRow(int row, boolean notify){
 		if (row<0 || row>= getNumberOfRows())
 			return false;
 		Taxa taxa = getProject().getTaxa(row);
-		getProject().removeFileElement(taxa);//must remove first, before disposing
+		getProject().removeFileElement(taxa, notify);//must remove first, before disposing
 		taxa.dispose();
 		return true;
 	}
diff --git a/Source/mesquite/lists/TaxonGroupList/TaxonGroupList.java b/Source/mesquite/lists/TaxonGroupList/TaxonGroupList.java
index e4af00f73..f81da50fd 100644
--- a/Source/mesquite/lists/TaxonGroupList/TaxonGroupList.java
+++ b/Source/mesquite/lists/TaxonGroupList/TaxonGroupList.java
@@ -284,7 +284,7 @@ public void setRowName(int row, String name){
 	}
 	public String getRowName(int row){
 		if (groups!=null){
-			if (row<0 && row >= groups.size())
+			if (row<0 || row >= groups.size())
 				return null;
 			return ((Listable)groups.elementAt(row)).getName();
 		}
diff --git a/Source/mesquite/lists/TreeblockList/TreeblockList.java b/Source/mesquite/lists/TreeblockList/TreeblockList.java
index abdaf2c38..0e4b2e9ce 100644
--- a/Source/mesquite/lists/TreeblockList/TreeblockList.java
+++ b/Source/mesquite/lists/TreeblockList/TreeblockList.java
@@ -19,6 +19,7 @@
 import java.util.*;
 import java.awt.*;
 import mesquite.lib.*;
+import mesquite.lib.characters.CharacterData;
 import mesquite.lib.duties.*;
 import mesquite.lib.table.*;
 
@@ -50,6 +51,14 @@ public boolean showing(Object obj){
 		return (getModuleWindow()!=null && obj == treeBlocks);
 	}
 
+	public boolean rowsShowable(){
+		return true;
+	}
+	public void showItemAtRow(int row){
+		TreeVector trees = (TreeVector)treeBlocks.elementAt(row);
+		trees.showMe();
+		
+	}
 	public boolean rowsDeletable(){
 		return true;
 	}
@@ -67,7 +76,7 @@ public boolean deleteRow(int row, boolean notify){
 		if (row<0 || row>= getNumberOfRows())
 			return false;
 		TreeVector trees = (TreeVector)treeBlocks.elementAt(row);
-		getProject().removeFileElement(trees);//must remove first, before disposing
+		getProject().removeFileElement(trees, notify);//must remove first, before disposing
 		trees.dispose();
 		return true;
 	}
diff --git a/Source/mesquite/lists/lib/CharMatricesListWindow.java b/Source/mesquite/lists/lib/CharMatricesListWindow.java
index 1a73387c2..67a491b83 100644
--- a/Source/mesquite/lists/lib/CharMatricesListWindow.java
+++ b/Source/mesquite/lists/lib/CharMatricesListWindow.java
@@ -4,6 +4,9 @@
 import java.awt.Graphics;
 
 import mesquite.lib.ListableVector;
+import mesquite.lib.Listenable;
+import mesquite.lib.MesquiteListener;
+import mesquite.lib.Notification;
 import mesquite.lib.characters.CharacterData;
 
 public class CharMatricesListWindow extends ListableVectorWindow {
@@ -21,6 +24,8 @@ public ListableVector getDatas() {
 	public void setDatas(ListableVector datas) {
 		this.datas = datas;
 	}
+	public void notifyRowDeletion(Object obj){ // row deletion notification happens through remove file element of project
+	}
 
 	/*...............................................................................................................*/
 	public void setRowNameColor(Graphics g, int row){
diff --git a/Source/mesquite/lists/lib/ListModule.java b/Source/mesquite/lists/lib/ListModule.java
index d866cb3d9..f50b130ca 100644
--- a/Source/mesquite/lists/lib/ListModule.java
+++ b/Source/mesquite/lists/lib/ListModule.java
@@ -134,6 +134,11 @@ public String getColumnExplanation(int column){
 	public boolean rowsDeletable(){
 		return false;
 	}
+	public boolean rowsShowable(){
+		return false;
+	}
+	public void showItemAtRow(int row){
+	}
 	public boolean rowsAddable(){
 		return false;
 	}
diff --git a/Source/mesquite/lists/lib/ListWindow.java b/Source/mesquite/lists/lib/ListWindow.java
index d279b89ba..4b4e4ceca 100644
--- a/Source/mesquite/lists/lib/ListWindow.java
+++ b/Source/mesquite/lists/lib/ListWindow.java
@@ -14,6 +14,9 @@
 package mesquite.lists.lib;
 
 import java.awt.*;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
 import java.awt.event.*;
 import java.util.*;
 
@@ -116,6 +119,9 @@ public ListWindow (ListModule ownerModule) {
 		//ownerModule.addMenuSeparator();
 		if (owner.rowsAddable())
 			ownerModule.addMenuItem( "Add " + owner.getItemTypeNamePlural() + "...", ownerModule.makeCommand("addRows", this));
+		if (owner.rowsShowable())
+			ownerModule.addMenuItem( "Show Selected " + owner.getItemTypeNamePlural(), showCommand = ownerModule.makeCommand("showSelectedRows", this));
+	
 		if (owner.rowsDeletable()) {
 			ownerModule.addMenuItem( "Delete Selected " + owner.getItemTypeNamePlural(), deleteCommand = ownerModule.makeCommand("deleteSelectedRows", this));
 			MesquiteWindow.addKeyListener(this, this);
@@ -124,6 +130,10 @@ public ListWindow (ListModule ownerModule) {
 			MesquiteMenuItemSpec mm = ownerModule.addMenuItem( "Move Selected " + owner.getItemTypeNamePlural() + " To...", ownerModule.makeCommand("moveSelectedTo", this));
 			mm.setShortcut(KeyEvent.VK_M);
 		}
+		MesquiteSubmenuSpec mss2 =	ownerModule.addSubmenu(null,"Select");
+		ownerModule.addItemToSubmenu(null, mss2, ownerModule.addMenuItem( "Invert Selection", ownerModule.makeCommand("invertSelection", this)));
+		ownerModule.addItemToSubmenu(null, mss2, ownerModule.addMenuItem( "Select by List in Clipboard", ownerModule.makeCommand("selectByClipboard", this)));
+
 		setShowExplanation(true);
 		setShowAnnotation(true);
 		table.requestFocusInWindow();
@@ -284,6 +294,7 @@ private void doWandTouch(String arguments){
 				if (arguments.indexOf("shift")<0 && !withinSelection && !deselects)
 					assoc.deselectAll();
 				table.offAllEdits();
+				int count = 0;
 				for (int i=0; i<table.getNumRows(); i++){
 					boolean satisfies = satisfiesCriteria(text, table.getMatrixText(column, i));
 					if (nonMatching.getValue())
@@ -299,7 +310,10 @@ else if (satisfies)
 					else if (satisfies) {
 						assoc.setSelected(i, !deselects);
 					}
+					if (assoc.getSelected(i))
+						count++;
 				}
+				ownerModule.logln("" + count + " items are now selected");
 				assoc.notifyListeners(this, new Notification(MesquiteListener.SELECTION_CHANGED));
 			}
 			else {
@@ -309,6 +323,7 @@ else if (satisfies) {
 				if (arguments.indexOf("shift")<0 && !withinSelection && !deselects)
 					table.deselectAll();
 				table.offAllEdits();
+				int count = 0;
 				for (int i=0; i<table.getNumRows(); i++){
 					boolean satisfies = satisfiesCriteria(text, table.getMatrixText(column, i));
 					if (nonMatching.getValue())
@@ -329,8 +344,11 @@ else if (satisfies) {
 							table.selectRow(i);
 						else
 							table.deselectRow(i);
-					} 
+					}
+					if (table.isRowSelected(i))
+						count++;
 				}
+				ownerModule.logln("" + count + " rows are now selected");
 				table.repaintAll();
 			}
 		}
@@ -443,6 +461,7 @@ else if (checker.compare(this.getClass(), "Sorts rows", "[column touched] [row t
 			UndoInstructions undoInstructions = new UndoInstructions(UndoInstructions.PARTS_MOVED,assoc);
 			undoInstructions.recordPreviousOrder(assoc);
 			UndoReference undoReference = new UndoReference(undoInstructions, ownerModule);
+			
 			if (column>=0 && row >=0) {
 				long[] fullChecksumBefore=null;
 				if (assoc instanceof CharacterData) {
@@ -462,7 +481,12 @@ else if (checker.compare(this.getClass(), "Sorts rows", "[column touched] [row t
 						swapParts(assoc, j, j+1, text);
 					}
 				}
-
+				if (assoc instanceof ListableVector && ((ListableVector)assoc).size()>0){
+					Listable obj = ((ListableVector)assoc).elementAt(0);
+					mesquite.lib.duties.ElementManager m = ownerModule.findElementManager(obj.getClass());
+					if (m != null)
+						m.elementsReordered((ListableVector)assoc);
+				}
 				processPostSwap(assoc);
 				assoc.notifyListeners(this, new Notification(MesquiteListener.PARTS_MOVED, undoReference));
 				if (assoc instanceof CharacterData){
@@ -471,6 +495,7 @@ else if (checker.compare(this.getClass(), "Sorts rows", "[column touched] [row t
 				}
 			}
 			else if (column == -1 && row >=0) { //row names selected; sort by name
+				
 				long[] fullChecksumBefore=null;
 				if (assoc instanceof CharacterData) {
 					fullChecksumBefore = ((CharacterData)assoc).getIDOrderedFullChecksum();
@@ -487,6 +512,12 @@ else if (checker.compare(this.getClass(), "Sorts rows", "[column touched] [row t
 						swapParts(assoc, j, j+1, text);
 					}
 				}
+				if (assoc instanceof ListableVector && ((ListableVector)assoc).size()>0){
+					Listable obj = ((ListableVector)assoc).elementAt(0);
+					mesquite.lib.duties.ElementManager m = ownerModule.findElementManager(obj.getClass());
+					if (m != null)
+						m.elementsReordered((ListableVector)assoc);
+				}
 				assoc.notifyListeners(this, new Notification(MesquiteListener.PARTS_MOVED, undoReference));
 				if (assoc instanceof CharacterData){
 					long[] fullChecksumAfter = ((CharacterData)assoc).getIDOrderedFullChecksum();
@@ -494,8 +525,50 @@ else if (checker.compare(this.getClass(), "Sorts rows", "[column touched] [row t
 				}
 			}
 		}
+		else if (checker.compare(this.getClass(), "Shows the selected rows", null, commandName, "showSelectedRows")) {
+			showSelectedRows();
+			return null;
+		}
 		else if (checker.compare(this.getClass(), "Deletes the selected rows", null, commandName, "deleteSelectedRows")) {
 			deleteSelectedRows(true);
+			return null;
+		}
+		else if (checker.compare(this.getClass(), "Inverts which rows are selected", null, commandName, "invertSelection")) {
+			for (int im = 0; im < table.getNumRows(); im++){
+				if (table.isRowSelected(im)){
+					table.deselectRow(im); //2019: why this doesn't handle associable deselection, don't remember!
+					if (table.getRowAssociable() != null){
+						table.getRowAssociable().setSelected(im, false);
+					}
+				}
+				else
+					table.selectRow(im);
+			}
+			table.repaintAll();
+		}
+		else if (checker.compare(this.getClass(), "Select by List in Clipboard", null, commandName, "selectByClipboard")) {
+			String[] clipboard = null; //{"uce-101", "uce-1084"};
+			clipboard = null;
+			Clipboard clip = Toolkit.getDefaultToolkit().getSystemClipboard();
+			Transferable t = clip.getContents(this);
+			try {
+
+				String s = (String) t.getTransferData(DataFlavor.stringFlavor);
+				if (s != null) {
+					clipboard = StringUtil.getLines(s);
+				}
+			} catch (Exception e) {
+				e.printStackTrace();
+			}
+			for (int im = 0; im < table.getNumRows(); im++){
+				if (StringArray.indexOf(clipboard, table.getRowNameTextForDisplay(im))>=0){
+					table.selectRow(im);
+				if (table.getRowAssociable() != null)
+					table.getRowAssociable().setSelected(im, true);
+				}
+			}
+			table.repaintAll();
+
 		}
 		else if (checker.compare(this.getClass(), "Moves the selected rows ", "[row to move after; -1 if at start]", commandName, "moveSelectedTo")) {
 			if (!owner.rowsMovable())
@@ -574,7 +647,7 @@ void swapParts(Associable assoc, int first, int second, String[] text){
 		String temp = text[first];
 		text[first] = text[second];
 		text[second] = temp;
-		assoc.swapParts(first, second); 
+		assoc.swapParts(first, second, false); 
 	}
 	public void processPostSwap(Associable assoc){
 	}
@@ -876,6 +949,14 @@ public void addRows(int num) {
 		MenuOwner.decrementMenuResetSuppression();
 
 	}
+	public void showSelectedRows() {
+		int numSelected = 0;
+		for (int ic = table.getNumRows()-1; ic>=0; ic--){
+			if (table.isRowSelected(ic)) { 
+				owner.showItemAtRow(ic);
+			}
+		}
+	}
 	public void deleteSelectedRows(boolean byCommand) {
 		int numSelected = 0;
 		for (int ic = table.getNumRows()-1; ic>=0; ic--){
@@ -896,28 +977,13 @@ public void deleteSelectedRows(boolean byCommand) {
 			MenuOwner.incrementMenuResetSuppression();
 			if (ownerModule != null && ownerModule.getProject() != null)
 				ownerModule.getProject().incrementProjectWindowSuppression();
-			/*int[] which = new int[numSelected];
-			int howMany = 0;
-			for (int ic = table.getNumRows()-1; ic>=0; ic--){
-				if (table.isRowSelected(ic)) {
-		 			if (!owner.rowDeletable(ic)){
-			 			if (!MesquiteThread.isScripting())
-			 				owner.alert("Sorry, you can't delete that");
-			 		}
-			 		else {
-						which[howMany]=ic;
-						howMany++;
-					}
-				}
-			}
-			 */
+			
 
 			int count =0;
 			int currentNumRows = owner.getNumberOfRows();
 			Object obj = getCurrentObject();
 
 			//NOTE: this code allows reporting of what contiguous blocks were deleted, but causes full recalculations for each discontiguity
-
 			int row = currentNumRows-1;
 			int firstInBlockDeleted = -1;
 			int lastInBlockDeleted = -1;
@@ -951,51 +1017,8 @@ public void deleteSelectedRows(boolean byCommand) {
 				}
 				row--;
 			}
-
-
-			/*				int firstInBlockDeleted = -1;
-				int lastInBlockDeleted = -1;
-				for (int ic = 0; ic<howMany; ic++){
-					if (lastInBlockDeleted < 0) {
-						lastInBlockDeleted = which[ic];
-						firstInBlockDeleted = lastInBlockDeleted;
-					}
-					else if (which[ic] == firstInBlockDeleted-1){ //still contiguous
-						firstInBlockDeleted = which[ic];					
-					}
-					else {
-						owner.deleteRows(firstInBlockDeleted, lastInBlockDeleted, false);
-						count += lastInBlockDeleted-firstInBlockDeleted+1;
-						lastInBlockDeleted = which[ic];
-						firstInBlockDeleted = lastInBlockDeleted;
-					}
-				}
-				if (lastInBlockDeleted>=0){
-					owner.deleteRows(firstInBlockDeleted, lastInBlockDeleted, false);
-					count += lastInBlockDeleted-firstInBlockDeleted+1;
-				}
-			 */
-
-			/*  old code pre-2. 02
-				int firstInBlockDeleted = -1;
-				for (int ic = 0; ic<howMany; ic++){
-					//NOTE: this code allows reporting of what contiguous blocks were deleted, but caused  full recalculations for each discontiguity
-					if (notifyInBlocks && obj instanceof Associable && firstInBlockDeleted < 0) {
-						firstInBlockDeleted = which[ic];
-					}
-			 		if (owner.deleteRow(which[ic], false))
-						count++;
-					//NOTE: this code allows reporting of what contiguous blocks were deleted, but caused  full recalculations for each discontiguity
-					if (notifyInBlocks && obj instanceof Associable && (ic+1 >= howMany || which[ic+1] != which[ic]-1)){ //next one is not adjacent; notify listeners
-						((Listenable)obj).notifyListeners(this, new Notification(MesquiteListener.PARTS_DELETED, new int[] {which[ic], firstInBlockDeleted - which[ic]+1}));
-						((Listenable)obj).decrementNotifySuppress();
-						((Listenable)obj).incrementNotifySuppress();
-						firstInBlockDeleted = -1;
-					}
-				}
-			 */
-
 			table.setNumRows(currentNumRows-count);
+
 			//NOTE: this code allows reporting of what contiguous blocks were deleted, but causes full recalculations for each discontiguity
 			notifyRowDeletion(obj);
 			table.repaintAll();
diff --git a/Source/mesquite/meristic/lib/MeristicData.java b/Source/mesquite/meristic/lib/MeristicData.java
index 676003952..3a7cdef29 100644
--- a/Source/mesquite/meristic/lib/MeristicData.java
+++ b/Source/mesquite/meristic/lib/MeristicData.java
@@ -420,7 +420,7 @@ else if (starting>numChars)
 	}
 	/*..........................................MeristicData................*/
 	/**swaps characters first and second.*/
-	public boolean swapParts(int first, int second){
+	public boolean swapParts(int first, int second, boolean notify){
 		if (first<0 || first >= numChars)
 			return false;
 		if (second<0 || second >= numChars)
@@ -429,7 +429,7 @@ public boolean swapParts(int first, int second){
 			Integer2DArray oldMatrix = ((Integer2DArray)matrices.elementAt(item));
 			Integer2DArray.swapColumns(oldMatrix.getMatrix(), first, second);
 		}
-		return super.swapParts(first, second);
+		return super.swapParts(first, second, notify);
 	}
 	/*..........................................MeristicData................*/
 	/**moves num characters from position "first" to just after position "justAfter"; returns true iff successful.*/
diff --git a/Source/mesquite/minimal/BasicFileCoordinator/ProjectWindow.java b/Source/mesquite/minimal/BasicFileCoordinator/ProjectWindow.java
index ad7076754..c7799feba 100644
--- a/Source/mesquite/minimal/BasicFileCoordinator/ProjectWindow.java
+++ b/Source/mesquite/minimal/BasicFileCoordinator/ProjectWindow.java
@@ -459,31 +459,35 @@ int sequenceUpToDate(){
 				panel.repaint();
 				e++;
 				if (proj.getNumberCharMatricesVisible(t)>0){
-					for (int k = 0; k<proj.getNumberCharMatricesVisible(t) && elementInBounds(k, "character matrices"); k++){   
-						CharacterData data = proj.getCharacterMatrixVisible(t, k);
-						if (data.isUserVisible()){
+					e++; //for the title "Character Matrices"
+					if (proj.getNumberCharMatricesVisible(t)<=FileCoordinator.maxLinesOfMatricesTreeBlocksSeparateInPanel)
+						for (int k = 0; k<proj.getNumberCharMatricesVisible(t) && elementInBounds(k, "character matrices"); k++){   
+							CharacterData data = proj.getCharacterMatrixVisible(t, k);
+							if (data.isUserVisible()){
+								if (e>= elements.size())
+									return 5;
+								panel = ((ProjPanelPanel)elements.elementAt(e));
+								if (!(panel instanceof ElementPanel) || ((ElementPanel)panel).element != data || !panel.upToDate())
+									return 6;
+								panel.resetTitle();
+								panel.repaint();
+								e++;
+							}
+						}
+				}
+				if (proj.getNumberOfFileElements(TreeVector.class)>0){
+					e++; //for the title "Tree Blocks"
+					if (proj.getTreeVectors().size()<=FileCoordinator.maxLinesOfMatricesTreeBlocksSeparateInPanel)
+						for (int k = 0; k<proj.getNumberOfFileElements(TreeVector.class) && elementInBounds(k, "tree blocks"); k++){
+							TreeVector trees = (TreeVector)proj.getFileElement(TreeVector.class, k);
 							if (e>= elements.size())
-								return 5;
+								return 7;
 							panel = ((ProjPanelPanel)elements.elementAt(e));
-							if (!(panel instanceof ElementPanel) || ((ElementPanel)panel).element != data || !panel.upToDate())
-								return 6;
+							if (!(panel instanceof ElementPanel) || ((ElementPanel)panel).element != trees || !panel.upToDate())
+								return 8;
 							panel.resetTitle();
 							panel.repaint();
 							e++;
-						}
-					}
-				}
-				if (proj.getNumberOfFileElements(TreeVector.class)>0){
-					for (int k = 0; k<proj.getNumberOfFileElements(TreeVector.class) && elementInBounds(k, "tree blocks"); k++){
-						TreeVector trees = (TreeVector)proj.getFileElement(TreeVector.class, k);
-						if (e>= elements.size())
-							return 7;
-						panel = ((ProjPanelPanel)elements.elementAt(e));
-						if (!(panel instanceof ElementPanel) || ((ElementPanel)panel).element != trees || !panel.upToDate())
-							return 8;
-						panel.resetTitle();
-						panel.repaint();
-						e++;
 					}
 				}
 
@@ -637,23 +641,27 @@ public void refresh(){
 				addExtraPanel(panel = new TaxaPanel(bfc, this, w, t));
 				panel.setLocation(0,0);
 				if (proj.getNumberCharMatricesVisible(t)>0){
-					for (int k = 0; k<proj.getNumberCharMatricesVisible(t) && elementInBounds(k, "character matrices"); k++){
-						CharacterData data = proj.getCharacterMatrixVisible(t, k);
-						if (data.isUserVisible()){
-							if (data instanceof MolecularData)
-								addExtraPanel(panel = new MolecMPanel(bfc, this, w,data));
-							else if (data instanceof ContinuousData)
-								addExtraPanel(panel = new ContMPanel(bfc, this, w, data));
-							else if (data instanceof MeristicData)
-								addExtraPanel(panel = new MeristicMPanel(bfc, this, w, data));
-							else
-								addExtraPanel(panel = new CategMPanel(bfc, this, w, data));
-							panel.setLocation(0,0);
+					addExtraPanel(panel = new AbundanceMPanel(bfc, this, w, proj, t));
+					if (proj.getNumberCharMatricesVisible(t)<=FileCoordinator.maxLinesOfMatricesTreeBlocksSeparateInPanel)
+						for (int k = 0; k<proj.getNumberCharMatricesVisible(t) && elementInBounds(k, "character matrices"); k++){
+							CharacterData data = proj.getCharacterMatrixVisible(t, k);
+							if (data.isUserVisible()){
+								if (data instanceof MolecularData)
+									addExtraPanel(panel = new MolecMPanel(bfc, this, w,data));
+								else if (data instanceof ContinuousData)
+									addExtraPanel(panel = new ContMPanel(bfc, this, w, data));
+								else if (data instanceof MeristicData)
+									addExtraPanel(panel = new MeristicMPanel(bfc, this, w, data));
+								else
+									addExtraPanel(panel = new CategMPanel(bfc, this, w, data));
+								panel.setLocation(0,0);
+							}
 						}
-					}
 				}
-				if (proj.getNumberOfFileElements(TreeVector.class)>0){
-					for (int k = 0; k<proj.getNumberOfFileElements(TreeVector.class) && elementInBounds(k, "tree blocks"); k++){
+				if (proj.getTreeVectors().size()>0){
+					addExtraPanel(panel = new AbundanceTPanel(bfc, this, w, proj, t));
+					if (proj.getTreeVectors().size()<=FileCoordinator.maxLinesOfMatricesTreeBlocksSeparateInPanel)
+						for (int k = 0; k<proj.getNumberOfFileElements(TreeVector.class) && elementInBounds(k, "tree blocks"); k++){
 						TreeVector trees = (TreeVector)proj.getFileElement(TreeVector.class, k);
 						if (trees.getTaxa() == t){
 							addExtraPanel(panel = new TreesRPanel(bfc, this, w, trees));
@@ -1290,6 +1298,41 @@ public String getShowMatrixIconFileName(){ //for small 16 pixel icon at left of
 	}
 }
 /*======================================================================== */
+class AbundanceMPanel extends ElementPanel {
+	MesquiteProject project = null;
+	Taxa taxa = null;
+	public AbundanceMPanel(BasicFileCoordinator bfc, ClosablePanelContainer container,MesquiteWindow w,  MesquiteProject project, Taxa taxa){
+		super(bfc, container, w,project.getCharacterMatrices());
+		addCommand(true, null, "View List", "View List", new MesquiteCommand("showMe", project.getCharacterMatrices()));
+		this.taxa = taxa;
+		this.project = project;
+	}
+	public String getTitle(){
+		int n = project.getNumberCharMatricesVisible(taxa);
+		if (n>1)
+			return Integer.toString(n) + " Character Matrices";
+		return "Character Matrix";
+
+	}
+}
+/*======================================================================== */
+class AbundanceTPanel extends ElementPanel {
+	MesquiteProject project = null;
+	Taxa taxa = null;
+	public AbundanceTPanel(BasicFileCoordinator bfc, ClosablePanelContainer container,MesquiteWindow w,  MesquiteProject project, Taxa taxa){
+		super(bfc, container, w,project.getTreeVectors());
+		addCommand(true, null, "View List", "View List", new MesquiteCommand("showMe", project.getTreeVectors()));
+		this.taxa = taxa;
+		this.project = project;
+	}
+	public String getTitle(){
+		int n = project.getNumberTreeVectors(taxa);
+		if (n>1)
+			return Integer.toString(n) + " Tree Blocks";
+		return "Tree Block";
+	}
+}
+/*======================================================================== */
 class TreesRPanel extends ElementPanel {
 
 	public TreesRPanel(BasicFileCoordinator bfc, ClosablePanelContainer container, MesquiteWindow w, FileElement element){
diff --git a/Source/mesquite/minimal/Defaults/Defaults.java b/Source/mesquite/minimal/Defaults/Defaults.java
index 26919b323..ed2e5698f 100644
--- a/Source/mesquite/minimal/Defaults/Defaults.java
+++ b/Source/mesquite/minimal/Defaults/Defaults.java
@@ -108,7 +108,8 @@ public boolean startJob(String arguments, Object condition, boolean hiredByName)
 		sm.setFilterable(false);
 		MesquiteTrunk.mesquiteTrunk.addItemToSubmenu(MesquiteTrunk.fileMenu, MesquiteTrunk.defaultsSubmenu, "-", null);
 
-		MesquiteTrunk.mesquiteTrunk.addMenuItem(MesquiteTrunk.defaultsSubmenu,"Maximum # Items in Project Panel...", makeCommand("setProjectPanelMaxItems",  this));		
+		MesquiteTrunk.mesquiteTrunk.addMenuItem(MesquiteTrunk.defaultsSubmenu, "Max # Matrices/Tree Blocks Listed in Project Panel...", makeCommand("setProjectPanelMaxItemsSeparate",  this));
+		//MesquiteTrunk.mesquiteTrunk.addMenuItem(MesquiteTrunk.defaultsSubmenu,"Overall Max # Items in Project Panel...", makeCommand("setProjectPanelMaxItems",  this));		
 		sm = MesquiteTrunk.mesquiteTrunk.addSubmenu(MesquiteTrunk.defaultsSubmenu,"Project Panel Font Size", makeCommand("setProjectPanelFontSize",  this), MesquiteSubmenu.getFontSizeList());		
 		sm.setFilterable(false);
 		MesquiteTrunk.mesquiteTrunk.addCheckMenuItemToSubmenu(MesquiteTrunk.fileMenu, MesquiteTrunk.defaultsSubmenu,"Use File-Specific Project Panel Width", makeCommand("respectFileSpecificResourceWidth",  this), respectFileSpecificResourceWidth);
@@ -232,6 +233,10 @@ else if ("maxLinesOfAnyElementInPanel".equalsIgnoreCase(tag)) {
 			int m = MesquiteInteger.fromString(content);
 			FileCoordinator.maxLinesOfAnyElementInPanel = m;
 		}
+		else if ("maxLinesOfMatricesTreeBlocksSeparateInPanel".equalsIgnoreCase(tag)) {
+			int m = MesquiteInteger.fromString(content);
+			FileCoordinator.maxLinesOfMatricesTreeBlocksSeparateInPanel = m;
+		}
 		/*	else if ("tilePopouts".equalsIgnoreCase(tag)){
 			tilePopouts.setValue(content);
 			MesquiteFrame.popIsTile = tilePopouts.getValue();
@@ -314,6 +319,7 @@ public String preparePreferencesForXML () {
 		StringUtil.appendXMLTag(buffer, 2, "resourcesFontSize", MesquiteFrame.resourcesFontSize);
 		StringUtil.appendXMLTag(buffer, 2, "maxLinesOfAnyElementInPanel", FileCoordinator.maxLinesOfAnyElementInPanel);
 		StringUtil.appendXMLTag(buffer, 2, "maxLinesOfAnyElementInPanelQueried", FileCoordinator.maxLinesOfAnyElementInPanelQueried);
+		StringUtil.appendXMLTag(buffer, 2, "maxLinesOfMatricesTreeBlocksSeparateInPanel", FileCoordinator.maxLinesOfMatricesTreeBlocksSeparateInPanel);
 		StringUtil.appendXMLTag(buffer, 2, "useOtherChoicesInMenus", useOtherChoices);   
 		StringUtil.appendXMLTag(buffer, 2, "suggestedDirectory", MesquiteTrunk.suggestedDirectory);
 		StringUtil.appendXMLTag(buffer, 2, "askSeed", askSeed);   
@@ -444,6 +450,15 @@ else if (checker.compare(getClass(), "Sets the maximum number of items of a part
 			FileCoordinator.maxLinesOfAnyElementInPanelQueried = true;
 			storePreferences();
 		}
+		else if (checker.compare(getClass(), "Sets the maximum number of Matrices or Tree Blocks shown separately in Project Panel", "[number]", commandName, "setProjectPanelMaxItemsSeparate")) {
+			int num = MesquiteInteger.fromFirstToken(arguments, new MesquiteInteger(0));
+			if (!MesquiteInteger.isCombinable(num))
+				num= MesquiteInteger.queryInteger(containerOfModule(), "Maximum items of Matrices or Tree Blocks shown separately in project panel", null, FileCoordinator.maxLinesOfMatricesTreeBlocksSeparateInPanel);
+			if (!MesquiteInteger.isCombinable(num))
+				return null;
+			FileCoordinator.maxLinesOfMatricesTreeBlocksSeparateInPanel = num;
+			storePreferences();
+		}
 		else if (checker.compare(getClass(), "Sets the font size of project panel", "[font size]", commandName, "setProjectPanelFontSize")) {
 			int fontSize = MesquiteInteger.fromFirstToken(arguments, new MesquiteInteger(0));
 			if (!MesquiteInteger.isCombinable(fontSize))
diff --git a/Source/mesquite/minimal/ManageTaxa/ManageTaxa.java b/Source/mesquite/minimal/ManageTaxa/ManageTaxa.java
index 2d1dc39e6..cd5c7130c 100644
--- a/Source/mesquite/minimal/ManageTaxa/ManageTaxa.java
+++ b/Source/mesquite/minimal/ManageTaxa/ManageTaxa.java
@@ -1052,7 +1052,7 @@ void setOrder(Taxa taxa, Taxa oTaxa){  //sets order of taxa to be same as oTaxa
 			if (!StringUtil.blank(id)){
 				int whichTaxon = taxa.findByUniqueID(id);
 				if (whichTaxon >=0 && whichTaxon!= ic) {
-					taxa.swapParts(ic, whichTaxon);
+					taxa.swapParts(ic, whichTaxon, true);
 					anyIDMoves = true;
 					//logln("Taxon " + (whichTaxon+1) + " moved into position " + (ic+1) + " (a)");
 				}
@@ -1062,7 +1062,7 @@ void setOrder(Taxa taxa, Taxa oTaxa){  //sets order of taxa to be same as oTaxa
 			for (int ic = 0; ic<taxa.getNumTaxa(); ic++){ //first reorder by id's
 				int whichTaxon = taxa.whichTaxonNumber(oTaxa.getTaxonName(ic));
 				if (whichTaxon >=0 && whichTaxon!= ic) {
-					taxa.swapParts(ic, whichTaxon);
+					taxa.swapParts(ic, whichTaxon, true);
 					//logln("Taxon " + (whichTaxon+1) + " moved into position " + (ic+1) + " (b)");
 				}
 			}
@@ -1080,7 +1080,7 @@ void restoreOrderIfNeeded(Taxa taxa){  //sets order of taxa to be same as unique
 			if (!StringUtil.blank(id)){
 				int whichTaxon = taxa.findByUniqueID(id);
 				if (whichTaxon >=0 && whichTaxon!= ic) {
-					taxa.swapParts(ic, whichTaxon);
+					taxa.swapParts(ic, whichTaxon, true);
 					anyIDMoves = true;
 					//logln("Taxon " + (whichTaxon+1) + " moved into position " + (ic+1) + " (a)");
 				}
@@ -1090,7 +1090,7 @@ void restoreOrderIfNeeded(Taxa taxa){  //sets order of taxa to be same as unique
 			for (int ic = 0; ic<taxa.getNumTaxa(); ic++){ //first reorder by id's
 				int whichTaxon = taxa.whichTaxonNumber(storedOrder[ic][1]);
 				if (whichTaxon >=0 && whichTaxon!= ic) {
-					taxa.swapParts(ic, whichTaxon);
+					taxa.swapParts(ic, whichTaxon, true);
 					//logln("Taxon " + (whichTaxon+1) + " moved into position " + (ic+1) + " (b)");
 				}
 			}
diff --git a/Source/mesquite/molec/AvgSequenceLengthMatrix/AvgSequenceLengthMatrix.java b/Source/mesquite/molec/AvgSequenceLengthMatrix/AvgSequenceLengthMatrix.java
index 536c28eb7..5d4e9e350 100644
--- a/Source/mesquite/molec/AvgSequenceLengthMatrix/AvgSequenceLengthMatrix.java
+++ b/Source/mesquite/molec/AvgSequenceLengthMatrix/AvgSequenceLengthMatrix.java
@@ -22,7 +22,6 @@ public void calculateNumber(MCharactersDistribution data, MesquiteNumber result,
 		if (result == null || data == null)
 			return;
 		clearResultAndLastResult(result);
-
 		CharacterData parentData = data.getParentData();
 		if (parentData == null){
 			if (resultString != null)
diff --git a/Source/mesquite/molec/ColorByAA/ColorByAA.java b/Source/mesquite/molec/ColorByAA/ColorByAA.java
index c5526f4c2..186856e86 100644
--- a/Source/mesquite/molec/ColorByAA/ColorByAA.java
+++ b/Source/mesquite/molec/ColorByAA/ColorByAA.java
@@ -107,7 +107,7 @@ public String getCellExplanation(int ic, int it){
   			s= "Codon position: " + i;
 		long aa = data.getAminoAcid(ic,it,true);
 		if (aa!=CategoricalState.inapplicable)
-			s += "Amino acid: " + ProteinState.toString(aa, false);
+			s += ", Amino acid: " + ProteinState.toString(aa, null, 0, false, false);
 		return s;
 	}
 	public String getCellString(int ic, int it){
diff --git a/Source/mesquite/molec/GapsToFromMissing/GapsToFromMissing.java b/Source/mesquite/molec/GapsToFromMissing/GapsToFromMissing.java
index a6e351f99..d62700d36 100644
--- a/Source/mesquite/molec/GapsToFromMissing/GapsToFromMissing.java
+++ b/Source/mesquite/molec/GapsToFromMissing/GapsToFromMissing.java
@@ -124,7 +124,7 @@ public synchronized boolean alterData(CharacterData dData, MesquiteTable table,
 				int startOfFirstDataRegion = -1;
 				int endOfLastDataRegion = -1;
 				for (int ic = 0; ic<data.getNumChars() && !done; ic++){  //the first terminal region
-					if (cellToConvert(data, ic, it)) {
+					if (cellToConvert(data, ic, it)) {  // this is a cell that fits the criteria in terms of is gap to convert or is missing to convert
 						if (mode==ALLREGIONS || mode==TERMINALREGION) {
 							data.setState(ic, it, conversionValue());
 							if (!MesquiteLong.isCombinable(numCellsAltered))
@@ -132,7 +132,7 @@ public synchronized boolean alterData(CharacterData dData, MesquiteTable table,
 							numCellsAltered++;
 						}
 					}
-					else if (!data.isUnassigned(ic, it)){  // we are out of the first terminal region
+					else if (!data.isUnassigned(ic, it) && !data.isInapplicable(ic, it)){  // we are out of the first terminal region
 						done = true;
 						startOfFirstDataRegion=ic;
 					}
@@ -148,7 +148,7 @@ else if (!data.isUnassigned(ic, it)){  // we are out of the first terminal regio
 								numCellsAltered++;
 							}
 						}
-						else if (!data.isUnassigned(ic, it)) {  // we are out of the end terminal region
+						else if (!data.isUnassigned(ic, it)&& !data.isInapplicable(ic, it)) {  // we are out of the end terminal region
 							endOfLastDataRegion=ic;
 							done = true;
 						}
diff --git a/Source/mesquite/molec/TaxaListHasData/TaxaListHasData.java b/Source/mesquite/molec/TaxaListHasData/TaxaListHasData.java
index 6606fab7c..ac0e5c976 100644
--- a/Source/mesquite/molec/TaxaListHasData/TaxaListHasData.java
+++ b/Source/mesquite/molec/TaxaListHasData/TaxaListHasData.java
@@ -331,7 +331,7 @@ else if (checker.compare(this.getClass(), "", null, commandName, "sortByPresence
 			for (int i=0; i<taxa.getNumberOfParts(); i++) {
 				if (bits.isBitOn(i)){
 					if (i>lowestYes+1){ //a "yes" that is deeper than last
-						taxa.swapParts(lowestYes+1, i);
+						taxa.swapParts(lowestYes+1, i, true);
 						lowestYes = lowestYes+1;
 					}
 					else
diff --git a/Source/mesquite/treefarm/CopyTreesToNexusBlock/CopyTreesToNexusBlock.java b/Source/mesquite/treefarm/CopyTreesToNexusBlock/CopyTreesToNexusBlock.java
new file mode 100644
index 000000000..542259ba9
--- /dev/null
+++ b/Source/mesquite/treefarm/CopyTreesToNexusBlock/CopyTreesToNexusBlock.java
@@ -0,0 +1,127 @@
+/* Mesquite source code.  Copyright 1997 and onward, W. Maddison and D. Maddison. 
+
+
+
+Disclaimer:  The Mesquite source code is lengthy and we are few.  There are no doubt inefficiencies and goofs in this code. 
+The commenting leaves much to be desired. Please approach this source code with the spirit of helping out.
+Perhaps with your help we can be more than a few, and make Mesquite better.
+
+Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.
+Mesquite's web site is http://mesquiteproject.org
+
+This source code and its compiled class files are free and modifiable under the terms of 
+GNU Lesser General Public License.  (http://www.gnu.org/copyleft/lesser.html)
+ */
+package mesquite.treefarm.CopyTreesToNexusBlock; 
+
+import java.awt.FileDialog;
+
+import mesquite.lib.*;
+import mesquite.lib.characters.CharacterData;
+import mesquite.lib.duties.*;
+
+/* ======================================================================== */
+public class CopyTreesToNexusBlock extends FileProcessor {
+	String saveFile = null;
+	/*.................................................................................................................*/
+	public boolean startJob(String arguments, Object condition, boolean hiredByName) {
+		return true;
+	}
+	/*.................................................................................................................*/
+	/** returns whether this module is requesting to appear as a primary choice */
+	public boolean requestPrimaryChoice(){
+		return false;  
+	}
+	/*.................................................................................................................*/
+	public boolean isPrerelease(){
+		return false;
+	}
+	/*.................................................................................................................*/
+	public boolean isSubstantive(){
+		return false; 
+	}
+
+	/** if returns true, then requests to remain on even after alterFile is called.  Default is false*/
+	public boolean pleaseLeaveMeOn(){
+		return false;
+	}
+	
+	boolean initFile(){
+		MesquiteFileDialog fdlg= new MesquiteFileDialog(containerOfModule(), "Output File for Tree(s)", FileDialog.SAVE);
+		fdlg.setBackground(ColorTheme.getInterfaceBackground());
+		fdlg.setVisible(true);
+		String fileName=fdlg.getFile();
+		String directory=fdlg.getDirectory();
+		if (StringUtil.blank(fileName) || StringUtil.blank(directory))
+			return false;
+		saveFile = MesquiteFile.composePath(directory, fileName);
+		MesquiteFile.putFileContents(saveFile, "#NEXUS"  + StringUtil.lineEnding(), true);
+		MesquiteFile.appendFileContents(saveFile, "BEGIN TREES;"  + StringUtil.lineEnding(), true);
+		return true;
+	}
+	/*.................................................................................................................*/
+   	/** Called before processing a series of files.*/
+   	public  boolean beforeProcessingSeriesOfFiles(){
+		if (saveFile == null || okToInteractWithUser(CAN_PROCEED_ANYWAY, "Asking for file to save")){ //need to check if can proceed
+			return initFile();
+		}
+  		return true;
+   	}
+
+	/*.................................................................................................................*/
+	/** Called to alter file. */
+	public boolean processFile(MesquiteFile file){
+		
+		if (saveFile == null || okToInteractWithUser(CAN_PROCEED_ANYWAY, "Asking for file to save")){ //need to check if can proceed
+			return initFile();
+		}
+		if (saveFile == null)
+			return false;
+		Listable[] treeVectors = proj.getFileElements(TreeVector.class);	
+   		if (treeVectors == null)
+   			return false;
+		for (int im = 0; im < treeVectors.length; im++){
+   			TreeVector trees = (TreeVector)treeVectors[im];
+   			if (trees.getFile() == file){
+   				for (int itree = 0; itree < trees.size(); itree++){
+   					Tree t = trees.getTree(itree);
+   					String description = t.writeTree(Tree.BY_NAMES);
+   					MesquiteFile.appendFileContents(saveFile, "TREE 'tree " + (itree+1) + " from file " + file.getFileName() + "' =  " , true);
+  					
+   					MesquiteFile.appendFileContents(saveFile, description + StringUtil.lineEnding(), true);
+  				}
+   			}
+   		}
+		return true;
+
+	}
+	/*.................................................................................................................*/
+   	/** Called after processing a series of files.*/
+   	public  boolean afterProcessingSeriesOfFiles(){
+		if (saveFile == null)
+			return false;
+		MesquiteFile.appendFileContents(saveFile, StringUtil.lineEnding() + "END;"  + StringUtil.lineEnding(), true);
+		return true;
+   	}
+   	
+   	/*.................................................................................................................*/
+	/** returns the version number at which this module was first released.  If 0, then no version number is claimed.  If a POSITIVE integer
+	 * then the number refers to the Mesquite version.  This should be used only by modules part of the core release of Mesquite.
+	 * If a NEGATIVE integer, then the number refers to the local version of the package, e.g. a third party package*/
+	public int getVersionOfFirstRelease(){
+		return 361;  
+	}
+
+	/*.................................................................................................................*/
+	public String getName() {
+		return "Compile Trees in Nexus Block in file";
+	}
+	/*.................................................................................................................*/
+	/** returns an explanation of what the module does.*/
+	public String getExplanation() {
+		return "Compiles trees from this file into a text file with a nexus tree block." ;
+	}
+
+}
+
+
diff --git a/Source/mesquite/treefarm/CopyTreesToSimpleFile/CopyTreesToSimpleFile.java b/Source/mesquite/treefarm/CopyTreesToSimpleFile/CopyTreesToSimpleFile.java
index 716db0f82..416aa26ae 100644
--- a/Source/mesquite/treefarm/CopyTreesToSimpleFile/CopyTreesToSimpleFile.java
+++ b/Source/mesquite/treefarm/CopyTreesToSimpleFile/CopyTreesToSimpleFile.java
@@ -65,6 +65,7 @@ public boolean processFile(MesquiteFile file){
 		Listable[] treeVectors = proj.getFileElements(TreeVector.class);	
    		if (treeVectors == null)
    			return false;
+		MesquiteFile.putFileContents(saveFile, "[trees from Process Data Files]  " , true);
 		for (int im = 0; im < treeVectors.length; im++){
    			TreeVector trees = (TreeVector)treeVectors[im];
    			if (trees.getFile() == file){
@@ -90,12 +91,12 @@ public int getVersionOfFirstRelease(){
 
 	/*.................................................................................................................*/
 	public String getName() {
-		return "Put Trees into Simple File";
+		return "Compile Trees into Simple File";
 	}
 	/*.................................................................................................................*/
 	/** returns an explanation of what the module does.*/
 	public String getExplanation() {
-		return "Puts trees from this file into a simple text file." ;
+		return "Compiles trees from this file into a simple text file." ;
 	}
 
 }
diff --git a/Source/mesquite/treefarm/FAFillTreeBlock/FAFillTreeBlock.java b/Source/mesquite/treefarm/FAFillTreeBlock/FAFillTreeBlock.java
index 7aa7d46c8..2d84c7619 100644
--- a/Source/mesquite/treefarm/FAFillTreeBlock/FAFillTreeBlock.java
+++ b/Source/mesquite/treefarm/FAFillTreeBlock/FAFillTreeBlock.java
@@ -117,7 +117,7 @@ public boolean processFile(MesquiteFile file){
 	}
 	/*.................................................................................................................*/
 	public String getName() {
-		return "Add and Fill Tree Block";
+		return "Make Trees and Add to File";
 	}
 	/*.................................................................................................................*/
 	/** returns an explanation of what the module does.*/
diff --git a/Source/mesquite/trees/BasicTreeWindowMaker/BasicTreeWindowMaker.java b/Source/mesquite/trees/BasicTreeWindowMaker/BasicTreeWindowMaker.java
index 3143e988d..b2cc4f991 100644
--- a/Source/mesquite/trees/BasicTreeWindowMaker/BasicTreeWindowMaker.java
+++ b/Source/mesquite/trees/BasicTreeWindowMaker/BasicTreeWindowMaker.java
@@ -4253,7 +4253,9 @@ public void notifyExtrasOfFieldTouch(Graphics g, int x, int y, int modifiers) {
 	private void treeChanged(boolean notifyContextListeners) {
 		if (tree == null || previousTree == null || undoTree == null)
 			return;
-
+		if (MesquiteTrunk.debugMode){
+			treeDisplay.restartChain("BTW-treeChanged " + StringUtil.getDateTimeWithSeconds()); 
+		}
 		if (tree.upToDateWithTaxa() && previousTree.upToDateWithTaxa()) {
 			canUndo = true;
 		}
diff --git a/Source/mesquite/trees/ManageTrees/ManageTrees.java b/Source/mesquite/trees/ManageTrees/ManageTrees.java
index 18c7d9781..03f397c99 100644
--- a/Source/mesquite/trees/ManageTrees/ManageTrees.java
+++ b/Source/mesquite/trees/ManageTrees/ManageTrees.java
@@ -173,6 +173,8 @@ public void removeBlockListener(MesquiteListener ml){
 	public MesquiteModule showElement(FileElement e){
 		if (e instanceof TreeVector)
 			return showTreesList((TreeVector)e);
+		if (e == getProject().getTreeVectors())
+			return showTreeBlocks(null);
 		return null;
 	}
 	public void deleteElement(FileElement e){
@@ -284,7 +286,8 @@ void reviseListeners(){
 	/** A method called immediately after the file has been read in.*/
 	public void projectEstablished() {
 		getFileCoordinator().addMenuItem(MesquiteTrunk.treesMenu, "-", null);
-		MesquiteSubmenuSpec mmis = getFileCoordinator().addSubmenu(MesquiteTrunk.treesMenu, "List of Trees", makeCommand("showTrees",  this), treesVector);
+		checkTreesVector();
+		MesquiteSubmenuSpec mmis = getFileCoordinator().addSubmenu(MesquiteTrunk.treesMenu, "List of Trees", makeCommand("showTrees",  this), treesVector); 
 		mmis.setBehaviorIfNoChoice(MesquiteSubmenuSpec.ONEMENUITEM_ZERODISABLE);
 		getFileCoordinator().addMenuItem(MesquiteTrunk.treesMenu, "List of Tree Blocks", makeCommand("showTreeBlocks",  this));
 		getFileCoordinator().addMenuItem(MesquiteTrunk.treesMenu, "Delete Tree Blocks...", makeCommand("deleteTreeBlocks",  this));
@@ -548,25 +551,7 @@ else if (checker.compare(this.getClass(), "Saves copies of a series of tree bloc
 			}
 		}
 		else if (checker.compare(this.getClass(), "Shows a list of the stored tree blocks", null, commandName, "showTreeBlocks")) {
-			//Check to see if already has lister for this
-			boolean found = false;
-			for (int i = 0; i<getNumberOfEmployees(); i++) {
-				Object e=getEmployeeVector().elementAt(i);
-				if (e instanceof ManagerAssistant)
-					if ( ((ManagerAssistant)e).getName().equals("Tree Blocks List")) {
-						((ManagerAssistant)e).getModuleWindow().setVisible(true);
-						return e;
-					}
-			}
-			ManagerAssistant lister= (ManagerAssistant)hireNamedEmployee(ManagerAssistant.class, StringUtil.tokenize("Tree Blocks List"));
-			if (lister==null){
-				alert("Sorry, no module was found to list the tree blocks");
-				return null;
-			}
-			lister.showListWindow(null);
-			if (!MesquiteThread.isScripting() && lister.getModuleWindow()!=null)
-				lister.getModuleWindow().setVisible(true);
-			return lister;
+			return showTreeBlocks(arguments);
 		}
 		else if (checker.compare(this.getClass(), "Deletes tree blocks from the project", null, commandName, "deleteTreeBlocks")) {
 			Listable[] chosen = ListDialog.queryListMultiple(containerOfModule(), "Select Tree Blocks to Delete", "Select one or more tree blocks to be deleted", (String)null, "Delete", false, getProject().getTreeVectors(), (boolean[])null);
@@ -854,6 +839,28 @@ else if (checker.compare(this.getClass(), "Creates a new filled tree block (inte
 		return null;
 	}
 	/*-----------------------------------------------------------------*/
+	MesquiteModule showTreeBlocks(String arguments){
+		//Check to see if already has lister for this
+		boolean found = false;
+		for (int i = 0; i<getNumberOfEmployees(); i++) {
+			Object e=getEmployeeVector().elementAt(i);
+			if (e instanceof ManagerAssistant)
+				if ( ((ManagerAssistant)e).getName().equals("Tree Blocks List")) {
+					((ManagerAssistant)e).getModuleWindow().setVisible(true);
+					return (MesquiteModule)e;
+				}
+		}
+		ManagerAssistant lister= (ManagerAssistant)hireNamedEmployee(ManagerAssistant.class, StringUtil.tokenize("Tree Blocks List"));
+		if (lister==null){
+			alert("Sorry, no module was found to list the tree blocks");
+			return null;
+		}
+		lister.showListWindow(null);
+		if (!MesquiteThread.isScripting() && lister.getModuleWindow()!=null)
+			lister.getModuleWindow().setVisible(true);
+		return lister;
+	}
+	/*-----------------------------------------------------------------*/
 	void includeTreeFile(String commandName, String arguments, CommandChecker checker, boolean partial){
 		if (!partial){
 			MesquiteModule fCoord = getFileCoordinator();
diff --git a/Source/mesquite/trees/RatioLongestBranches/RatioLongestBranches.java b/Source/mesquite/trees/RatioLongestBranches/RatioLongestBranches.java
new file mode 100644
index 000000000..bdfd672b9
--- /dev/null
+++ b/Source/mesquite/trees/RatioLongestBranches/RatioLongestBranches.java
@@ -0,0 +1,90 @@
+/* Mesquite source code.  Copyright 1997 and onward, W. Maddison and D. Maddison. 
+
+
+Disclaimer:  The Mesquite source code is lengthy and we are few.  There are no doubt inefficiencies and goofs in this code. 
+The commenting leaves much to be desired. Please approach this source code with the spirit of helping out.
+Perhaps with your help we can be more than a few, and make Mesquite better.
+
+Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.
+Mesquite's web site is http://mesquiteproject.org
+
+This source code and its compiled class files are free and modifiable under the terms of 
+GNU Lesser General Public License.  (http://www.gnu.org/copyleft/lesser.html)
+*/
+package mesquite.trees.RatioLongestBranches;
+
+import mesquite.lib.*;
+import mesquite.lib.duties.*;
+
+/** this is a silly little module that can be used as a demonstration for NumberForTree modules */
+public class RatioLongestBranches extends NumberForTree {
+	MesquiteNumber nt;
+	/*.................................................................................................................*/
+	public boolean startJob(String arguments, Object condition, boolean hiredByName) {
+ 		nt= new MesquiteNumber();
+ 		return true;
+  	 }
+	/*.................................................................................................................*/
+   	 public boolean isSubstantive(){
+   	 	return true;
+   	 }
+	/*.................................................................................................................*/
+   	 public boolean isPrerelease(){
+   	 	return false;
+   	 }
+ 	/*.................................................................................................................*/
+ 	/** returns the version number at which this module was first released.  If 0, then no version number is claimed.  If a POSITIVE integer
+ 	 * then the number refers to the Mesquite version.  This should be used only by modules part of the core release of Mesquite.
+ 	 * If a NEGATIVE integer, then the number refers to the local version of the package, e.g. a third party package*/
+ 	public int getVersionOfFirstRelease(){
+ 		return 361;  
+ 	}
+	/*-----------------------------------------*/
+ 	public void getLongestBranches(Tree tree, int node, MesquiteDouble longest, MesquiteDouble secondLongest) {
+ 		double length = tree.getBranchLength(node);
+ 		if (tree.getRoot() != node && MesquiteDouble.isCombinable(length)){
+ 			double currentLongest = longest.getValue();
+ 			double currentSecondLongest = secondLongest.getValue();
+ 			if (!longest.isCombinable() || MesquiteDouble.lessThan(currentLongest, length, 0)){
+ 				longest.setValue(length);
+ 				secondLongest.setValue(currentLongest);
+ 			}
+ 			else if (!secondLongest.isCombinable() || MesquiteDouble.lessThan(currentSecondLongest, length, 0)){
+ 				secondLongest.setValue(length);
+ 			}
+ 		}
+ 			for (int d = tree.firstDaughterOfNode(node); tree.nodeExists(d); d = tree.nextSisterOfNode(d))
+ 				getLongestBranches(tree, d, longest, secondLongest);
+ 		
+ 	}
+	/*.................................................................................................................*/
+	public void calculateNumber(Tree tree, MesquiteNumber result, MesquiteString resultString) {
+    	 if (result==null || tree==null)
+    	 		return;
+    	clearResultAndLastResult(result);
+    	MesquiteDouble longest = new MesquiteDouble();
+    	MesquiteDouble secondLongest = new MesquiteDouble();
+    	getLongestBranches(tree, tree.getRoot(), longest, secondLongest);
+    	if (longest.isCombinable() && secondLongest.isCombinable() && secondLongest.getValue() != 0){
+		nt.setValue(longest.getValue()/secondLongest.getValue());
+		result.setValue(nt);
+		if (resultString!=null)
+			resultString.setValue("Ratio: "+ nt.toString());
+    	}
+		saveLastResult(result);
+		saveLastResultString(resultString);
+	}
+	/*.................................................................................................................*/
+	/*.................................................................................................................*/
+    	 public String getName() {
+		return "Ratio of Longest Branches";
+   	 }
+	/*.................................................................................................................*/
+	/*.................................................................................................................*/
+ 	/** returns an explanation of what the module does.*/
+ 	public String getExplanation() {
+ 		return "Gets the ratio of the two greatest branch lengths in a tree." ;
+   	 }
+   	 
+}
+
diff --git a/Source/mesquite/trees/SquareLineTree/SquareLineTree.java b/Source/mesquite/trees/SquareLineTree/SquareLineTree.java
index 7e6df43e1..7d4d9c1da 100644
--- a/Source/mesquite/trees/SquareLineTree/SquareLineTree.java
+++ b/Source/mesquite/trees/SquareLineTree/SquareLineTree.java
@@ -454,6 +454,11 @@ private   void drawClade(Tree tree, Graphics g, int node) {
 	/*_________________________________________________*/
 	public   void drawTree(Tree tree, int drawnRoot, Graphics g) {
 		if (MesquiteTree.OK(tree)) {
+			if (MesquiteTrunk.debugMode){
+				treeDisplay.reportChain("SquareLineTree "  + StringUtil.getDateTimeWithSeconds()); 
+				treeDisplay.enableChain(); //has to draw once, so this is called to start
+			}
+
 			if (tree.getNumNodeSpaces()!=numNodes)
 				resetNumNodes(tree.getNumNodeSpaces());
 			g.setColor(treeDisplay.branchColor);
diff --git a/Source/mesquite/trunk/AboutPanel.java b/Source/mesquite/trunk/AboutPanel.java
index 514004f58..531e374e7 100644
--- a/Source/mesquite/trunk/AboutPanel.java
+++ b/Source/mesquite/trunk/AboutPanel.java
@@ -53,7 +53,7 @@ public void paint(Graphics g) {
 			g.drawImage(InfoBar.prereleaseImage,3,3,(ImageObserver)this);
 		}
 		g.drawString("http://www.mesquiteproject.org", 5,210);
-		g.drawString("Copyright (c) 1997-2018 W. & D. Maddison.", 5,225);
+		g.drawString("Copyright (c) 1997-2019 W. & D. Maddison.", 5,225);
 		
 		MesquiteWindow.uncheckDoomed(this);
 	}
diff --git a/Source/mesquite/trunk/ClockWatcherThread.java b/Source/mesquite/trunk/ClockWatcherThread.java
index f5b8b0e9f..91efa5862 100644
--- a/Source/mesquite/trunk/ClockWatcherThread.java
+++ b/Source/mesquite/trunk/ClockWatcherThread.java
@@ -26,12 +26,26 @@ public class ClockWatcherThread extends Thread {
 	Mesquite mesquite;
 	static final int sleep = 1500;
 	static final int catnap = 50;
+	static final int numBoutsPerSleep = 10;
 	int sleepTime = sleep;
 	long lastTick = 0;
 	public ClockWatcherThread (Mesquite mesquite) {
 		this.mesquite = mesquite;
 		setPriority(Thread.MIN_PRIORITY);
 	}
+	
+	void doDelayedRepaints(){
+		//Repainting any window on special repaint queue
+		for (int iw = MesquiteWindow.delayedRepaintQueue.size()-1;  iw>=0; iw--){
+			MesquiteWindow w = (MesquiteWindow)MesquiteWindow.delayedRepaintQueue.elementAt(iw);
+			if (System.currentTimeMillis()>w.drqTime){ 
+				if (!w.disposed() && !w.disposing)
+					w.repaintAll();
+				MesquiteWindow.delayedRepaintQueue.remove(w); //done! remove
+			}
+		}
+	}
+	
 	public void run() {
 		long sleepCount = 0;
 		boolean reportThreads = false;
@@ -44,18 +58,28 @@ public void run() {
 				sleepCount = 0;
 			else
 				sleepCount++;
-			try {
-				Thread.sleep(sleepTime);  
-			}
-			catch (InterruptedException e){
-				Thread.currentThread().interrupt();
+			
+			//sleep is down in a series of bouts. This is a kludge to let some functions happen at each bout (delayed repaint) but others be after each sleep
+			for (int iBout = 0; iBout<numBoutsPerSleep; iBout++){
+				try {
+					Thread.sleep(sleepTime/numBoutsPerSleep);  
+					doDelayedRepaints();
+				}
+				catch (InterruptedException e){
+					Thread.currentThread().interrupt();
+				}
 			}
 			MesquiteTrunk.checkForResetCheckMenuItems();
+			
+			//Surveying windows to reset graphically after first shown (bugs in some macOS versions)
 			if (sleptLong || sleepCount % (sleep/catnap) == 1) {
 				MesquiteThread.surveyDoomedIndicators();
 				if (MesquiteTrunk.isMacOSX())
 					MesquiteThread.surveyNewWindows();
 			}
+			
+			
+			//Surveying threads for progressindicators, need to put up "command is executing"
 			MesquiteThread[] mThreads = new MesquiteThread[MesquiteThread.threads.size()];
 			try {
 				for (int i=0; i<mThreads.length; i++)
@@ -63,11 +87,7 @@ public void run() {
 			}
 			catch (Exception e){
 			}
-/*if (KeyboardFocusManager.getCurrentKeyboardFocusManager() != null && KeyboardFocusManager.getCurrentKeyboardFocusManager().getFocusOwner() != null){
-	System.out.println("" + KeyboardFocusManager.getCurrentKeyboardFocusManager().getFocusOwner().getClass());
-System.out.println("xxx " + MesquiteWindow.windowOfItem(KeyboardFocusManager.getCurrentKeyboardFocusManager().getFocusOwner()));
-}
-*/
+
 			sleepTime = sleep;
 			sleepCount++;
 			for (int i=0; i<mThreads.length && mThreads[i]!=null; i++){  //go through current threads
diff --git a/docs/Acknowledgements.html b/docs/Acknowledgements.html
index 197e50951..3c9c061e5 100644
--- a/docs/Acknowledgements.html
+++ b/docs/Acknowledgements.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Acknowledgements<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Additional Mesquite Packages.html b/docs/Additional Mesquite Packages.html
index 2b0c0c073..498e60bad 100644
--- a/docs/Additional Mesquite Packages.html	
+++ b/docs/Additional Mesquite Packages.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Additional Packages<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Align.html b/docs/Align.html
index ddcf165ed..25688ea1d 100644
--- a/docs/Align.html
+++ b/docs/Align.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Sequence Alignment<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Analyzing Continuous Characters.html b/docs/Analyzing Continuous Characters.html
index 37c94bfbc..5e5098ebe 100644
--- a/docs/Analyzing Continuous Characters.html	
+++ b/docs/Analyzing Continuous Characters.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Continuous characters<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Analyzing Molecular Data.html b/docs/Analyzing Molecular Data.html
index a55f21f3b..f7333722f 100644
--- a/docs/Analyzing Molecular Data.html	
+++ b/docs/Analyzing Molecular Data.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Molecular Data<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Ancestral States.html b/docs/Ancestral States.html
index eeefb38ca..db36c211f 100644
--- a/docs/Ancestral States.html	
+++ b/docs/Ancestral States.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Ancestral States<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
@@ -199,11 +199,13 @@ <h3>&nbsp;</h3>
     
     
 <h1 id="toc0"><a name="Studying the History of Character Evolution"></a>Studying the History of Character Evolution</h1>
- With a phylogenetic tree and a distribution of character states in the observed (terminal) taxa, Mesquite can attempt to reconstruct the character states at ancestral nodes. Two separate issues to consider are the method by which the reconstruction is done, and how its results are displayed to the user. Mesquite currently can use either parsimony, likelihood or Bayesian methods to reconstruct ancestral states, and has several display methods, including &quot;Trace Character History&quot; which paints the branches of the tree to show the reconstruction.<br />
-We recommend highly that you examine the example files provided in the folder &quot;Ancestral State Examples&quot;. The minimal configuration to use with these examples is &quot;Ancestral States&quot; (indicate this configuration under File&gt;Activate/Deactivate Packages&gt;Choose Configuration), but you can also leave Mesquite in its default All Installed Modules mode.<br />
-<div style="text-align: center"><img src="files/ancStates.gif" alt="ancStates.gif" title="ancStates.gif" /></div><br />
+ <p>With a phylogenetic tree and a distribution of character states in the observed (terminal) taxa, Mesquite can attempt to reconstruct the character states at ancestral nodes. Two separate issues to consider are the method by which the reconstruction is done, and how its results are displayed to the user. Mesquite currently can use either parsimony, likelihood or Bayesian methods to reconstruct ancestral states, and has several methods to present the results. One of these display methods is  &quot;Trace Character History&quot;, which paints the branches of the tree to show the reconstruction; some other tools give lists of ancestral states or changes in text.</p>
+ <p>We recommend highly that you begin your exploration of Mesquite's character evolution tools by going through the example files provided in the folder &quot;Ancestral State Examples&quot; (this is provided in the &quot;examples&quot; folder within Mesquite_Folder. Begin with file &quot;01-DataMatrix.nex, and then step through the examples.</p>
+ <p>These tools are enabled by default in Mesquite. If you do decide to alter Mesquite's configuration so that fewer modules are available, then the minimal configuration to use with these examples is &quot;Ancestral States&quot; (indicate this configuration under File&gt;Activate/Deactivate Packages&gt;Choose Configuration).<br />
+ </p>
+ <div style="text-align: center"><img src="files/ancStates.gif" alt="ancStates.gif" title="ancStates.gif" /></div><br />
 <h3 id="toc1"><a name="Studying the History of Character Evolution--Trace Character History"></a><a name="tch"></a>Trace Character History</h3>
- The Trace Character History facility graphically represents a history of character evolution on the tree. It is available under the Analysis:Tree menu of a tree window (e.g., the basic Tree Window, Dependent Tree Window, Mirror Tree Window, Multitree Window). If you select this you will probably be asked for a source of characters (e.g., stored characters) and areconstruction method (e.g., <a  href="Ancestral%20States.html#parsimony">parsimony</a>, <a  href="Ancestral%20States.html#likelihood">likelihood</a>, <a  href="Ancestral%20States.html#scm">stochastic character mapping</a>). (If you have &quot;Use Stored Characters/Matrices by Default&quot; turned on in the Defaults submenu if the File menu, Mesquite won't ask you and will simply use Stored Characters.) The tree will be painted to show ancestral states, and a trace legend will appear. The Trace Legend contains an important text area that gives details of the current ancestral state tracing. You can also see details of the reconstruction by switching the window to Text mode using the menu item Window&gt;View Modes&gt;Text.<br />
+ The Trace Character History facility graphically represents a history of character evolution on the tree. It is available under the Analysis:Tree menu of a tree window (e.g., the basic Tree Window, Dependent Tree Window, Mirror Tree Window, Multitree Window). If you select this you will probably be asked for a source of characters (e.g., stored characters) and a reconstruction method (e.g., <a  href="Ancestral%20States.html#parsimony">parsimony</a>, <a  href="Ancestral%20States.html#likelihood">likelihood</a>, <a  href="Ancestral%20States.html#scm">stochastic character mapping</a>). (If you have &quot;Use Stored Characters/Matrices by Default&quot; turned on in the Defaults submenu if the File menu, Mesquite won't ask you and will simply use Stored Characters.) The tree will be painted to show ancestral states, and a trace legend will appear. The Trace Legend contains an important text area that gives details of the current ancestral state tracing. You can also see details of the reconstruction by switching the window to Text mode using the menu item Window&gt;View Modes&gt;Text.<br />
 <br />
 For categorical and molecular data, you can change the colors used in Trace Character by double clicking on the color rectangle in the Trace Legend. Revert to Default Colors is available in the Trace menu.<br />
 <br />
diff --git a/docs/Are strepsipterans related to flies.html b/docs/Are strepsipterans related to flies.html
index 9aec5607c..0001f76a5 100644
--- a/docs/Are strepsipterans related to flies.html	
+++ b/docs/Are strepsipterans related to flies.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Hypothesis testing<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Beginning Mesquite.html b/docs/Beginning Mesquite.html
index 8b9f8fa62..8f9afa6e2 100644
--- a/docs/Beginning Mesquite.html	
+++ b/docs/Beginning Mesquite.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Beginning Mesquite<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Bugs and Troubleshooting.html b/docs/Bugs and Troubleshooting.html
index 0fe24d905..888118108 100644
--- a/docs/Bugs and Troubleshooting.html	
+++ b/docs/Bugs and Troubleshooting.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Bugs and Troubleshooting<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Character Evolution.html b/docs/Character Evolution.html
index fad422ca6..1ecf1abf9 100644
--- a/docs/Character Evolution.html	
+++ b/docs/Character Evolution.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Character Evolution<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Characters & Matrices.html b/docs/Characters & Matrices.html
index 21234c540..09acee7ed 100644
--- a/docs/Characters & Matrices.html	
+++ b/docs/Characters & Matrices.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Characters &amp; Matrices<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Charts.html b/docs/Charts.html
index 48da9f023..d322b21fc 100644
--- a/docs/Charts.html
+++ b/docs/Charts.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Charts<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Contact Us.html b/docs/Contact Us.html
index 81a081852..a80cd0478 100644
--- a/docs/Contact Us.html	
+++ b/docs/Contact Us.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Contact Us<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Developers Documentation.html b/docs/Developers Documentation.html
index a58016b70..2d3824c66 100644
--- a/docs/Developers Documentation.html	
+++ b/docs/Developers Documentation.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Developer's Documentation<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Developers Reference.html b/docs/Developers Reference.html
index fbfbe1cfc..049717230 100644
--- a/docs/Developers Reference.html	
+++ b/docs/Developers Reference.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Developer's Reference<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Development Team.html b/docs/Development Team.html
index ce66e3d12..d2b6e5c23 100644
--- a/docs/Development Team.html	
+++ b/docs/Development Team.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Development Team<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Diversification.html b/docs/Diversification.html
index a9d895e9e..44141c1e3 100644
--- a/docs/Diversification.html
+++ b/docs/Diversification.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Diversification<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Documenting Your Work.html b/docs/Documenting Your Work.html
index 80fd64167..f77d92553 100644
--- a/docs/Documenting Your Work.html	
+++ b/docs/Documenting Your Work.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Documenting Your Work<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Example Files.html b/docs/Example Files.html
index 0b9c07332..6a2dd26ce 100644
--- a/docs/Example Files.html	
+++ b/docs/Example Files.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Example Files<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/FAQ.html b/docs/FAQ.html
index af4ef6175..67bba4377 100644
--- a/docs/FAQ.html
+++ b/docs/FAQ.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->FAQ<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Files.html b/docs/Files.html
index 33149dc7c..77b27f631 100644
--- a/docs/Files.html
+++ b/docs/Files.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Files<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Gene Trees.html b/docs/Gene Trees.html
index a052de5f2..c0c6fc913 100644
--- a/docs/Gene Trees.html	
+++ b/docs/Gene Trees.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Gene Trees<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Getting Help.html b/docs/Getting Help.html
index ddec24038..09f34d12d 100644
--- a/docs/Getting Help.html	
+++ b/docs/Getting Help.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Getting Help<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Glossary.html b/docs/Glossary.html
index e435f49ae..ceeb828f5 100644
--- a/docs/Glossary.html
+++ b/docs/Glossary.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Glossary<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/History of Mesquite.html b/docs/History of Mesquite.html
index 4777d4cee..09678edca 100644
--- a/docs/History of Mesquite.html	
+++ b/docs/History of Mesquite.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->History of Mesquite<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/History of New Features.html b/docs/History of New Features.html
index 8a65d6f08..f01d6b012 100644
--- a/docs/History of New Features.html	
+++ b/docs/History of New Features.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->History of New Features<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
@@ -208,6 +208,40 @@ <h1 id="toc0"><a name="New Features, Bugs, and History of Features and Bug Fixes
   <a name="New Features, Bugs, and History of Features and Bug Fixes--Features in the next release version of Mesquite; the latest source code in the development branch of the MesquiteProject/MesquiteCore repository on GitHub contains these changes" id="New Features, Bugs, and History of Features and Bug Fixes--Features in the next release version of Mesquite; the latest source code in the development branch of the MesquiteProject/MesquiteCore repository on GitHub contains these changes"></a>Features to come in the next release version of Mesquite are listed <a href="https://github.com/MesquiteProject/MesquiteCore/wiki/New-features-and-bug-fixes-in-the-development-version">on this web page</a>. These new features and bug fixes are already contained in latest source code in the development branch of the MesquiteProject/MesquiteCore repository on GitHub.</p>
  <p>&nbsp;</p>
  <hr />
+ <h3>Next Version</h3>
+ <h4 id="toc84">New Features </h4>
+ <ul>
+   <li>None yet </li>
+ </ul>
+ <h4>Bug Fixes and Workarounds</h4>
+ <ul>
+   <li>None yet</li>
+ </ul>
+ <hr />
+ <h3>Version 3.61</h3>
+ <h4 id="toc83">New Features</h4>
+ <ul>
+   <li><strong>Refine Groups by Codon Position</strong> added (in List of Characters window, drop-down menu by touching on the title of the Groups column). This will create a new character partition that takes the current character partition, and if any existing group has different codon positions in it, will assign each codon position within that group to a separate group. For example, if you have two protein coding genes in the matrix, say Gene1 and Gene2, and the first 900 characters are assigned to a character group called Gene1, and the last 600 characters to a group called Gene2, and within each gene codon positions are specified, then using this tool there will be six group created: Gene1_1, for all of the first positions in Gene1, Gene1_2, for all the second positions in Gene1, and then similarly Gene1_3, Gene2_1, Gene2_2, and Gene2_3. </li>
+   <li>Added &quot;<strong>Select by List in Clipboard</strong>&quot; to List Windows.  If you have a list of names in the Clipboard (as text, one name per line), and go to the list window, and use this, it will select all rows in the list window whose names match a name in that list of names in the Clipboard.</li>
+   <li>Added ability to color cells and select rows based upon values in Character Matrix List Window</li>
+   <li>As a minor change, tree windows now have a default orientation of &quot;Right&quot;, i.e., with the root of the tree on the left and taxon names on the right. </li>
+   <li>The <strong>Project Panel</strong> (on the left of a Mesquite window) has been improved. Among other things, it now lists matrices and tree blocks only if there are less than a specified number (by default 16).</li>
+   <li>A few new calculators were added for taxa, matrices, and trees: <strong>Number of Matrices with Data for Taxon</strong> counts, for a taxon, in how many matrices the taxon has data. This can be used, e.g., to see how abundant is data for a taxon. <strong>Number of Selected Taxa with Data in Matrix</strong> counts, for a matrix, how many of the currently selected taxa have data in that matrix. This can be used, e.g. to filter matrices that are too sparsely represented by taxa. <strong>Ratio of Longest Branches</strong> calculates, for a tree, the ratio of the two longest branches in a tree. This can be used, e.g., to find trees suggesting paralogy.</li>
+   <li>Some functions (modules) used in Process Data Files were renamed for clarity.</li>
+   <li>Other minor improvements.</li>
+ </ul>
+ <br />
+ <strong> Bug Fixes and Workarounds</strong><br />
+ </p>
+ <ul>
+   <li>The List of Trees menu item was accidentally removed in version 3.6. Now restored.</li>
+   <li>Significantly increased the speed of matrix concatenation and general aspects of list windows, including sorting. </li>
+   <li>Fixed amino acid output in Trace All Changes</li>
+   <li>Corrected handling of terminal ? in Gaps to and from Missing alterer.</li>
+   <li>Copy/paste now works as expected in the Notes window.</li>
+   <li>Miscellaneous small bugs fixed.</li>
+ </ul>
+ <hr />
  <h3>Version 3.6</h3>
  <h4 id="toc82">New Features</h4>
  <ul>
diff --git a/docs/How Mesquite Works.html b/docs/How Mesquite Works.html
index 313902458..3d4322623 100644
--- a/docs/How Mesquite Works.html	
+++ b/docs/How Mesquite Works.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->How Mesquite Works<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/How to Cite Mesquite.html b/docs/How to Cite Mesquite.html
index 5dac4e763..102633d9c 100644
--- a/docs/How to Cite Mesquite.html	
+++ b/docs/How to Cite Mesquite.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->How to Cite Mesquite<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
@@ -213,8 +213,8 @@ <h2 id="toc1"><a name="How to cite Mesquite-Citing the software system in genera
 
 -->
 </style>
-<pre class="text">Maddison, W. P. and D.R. Maddison. 2018. Mesquite: a modular system for
-     evolutionary analysis.  Version 3.51  http://www.mesquiteproject.org</pre>
+<pre class="text">Maddison, W. P. and D.R. Maddison. 2019. Mesquite: a modular system for
+     evolutionary analysis.  Version 3.61  http://www.mesquiteproject.org</pre>
 
 (The version number listed above might not be up to date. Check the Mesquite Startup window or the Project and Files window when Mesquite is running to find the version you have.)<br />
 <br />
@@ -234,7 +234,7 @@ <h2 id="toc2"><a name="How to cite Mesquite-Citing the documentation"></a>Citing
 
 -->
 </style>
-<pre class="text">The Mesquite Project Team. 2018. Documentation for Mesquite: a modular system for
+<pre class="text">The Mesquite Project Team. 2019. Documentation for Mesquite: a modular system for
      evolutionary analysis.  http://www.mesquiteproject.org</pre>
 
 <br />
@@ -260,7 +260,7 @@ <h2 id="toc3"><a name="How to cite Mesquite-Citing Mesquite for analyses done"><
      version 3.5.
 &nbsp;
 Maddison, W. P. and D.R. Maddison. 2018. Mesquite: a modular system for
-     evolutionary analysis.  Version 3.51 http://www.mesquiteproject.org.
+     evolutionary analysis.  Version 3.61 http://www.mesquiteproject.org.
 &nbsp;
 Za, T. 2014. SimSpeciation: a package of modules to simulate evolutionary
      trees. Version 3.14159.</pre>
diff --git a/docs/Installation on Linux.html b/docs/Installation on Linux.html
index f99644f4a..2146d7941 100644
--- a/docs/Installation on Linux.html	
+++ b/docs/Installation on Linux.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Installation on Linux<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Installation on MacOS X.html b/docs/Installation on MacOS X.html
index f3df78d65..402c326b6 100644
--- a/docs/Installation on MacOS X.html	
+++ b/docs/Installation on MacOS X.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Installation on MacOS X<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Installation on Windows.html b/docs/Installation on Windows.html
index 8fe872e41..7d2b49cb5 100644
--- a/docs/Installation on Windows.html	
+++ b/docs/Installation on Windows.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Installation on Windows<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Installation.html b/docs/Installation.html
index f071a53fc..3a83212ca 100644
--- a/docs/Installation.html
+++ b/docs/Installation.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Installation<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Installing Mesquite Packages.html b/docs/Installing Mesquite Packages.html
index 31aec17cf..758eab4b0 100644
--- a/docs/Installing Mesquite Packages.html	
+++ b/docs/Installing Mesquite Packages.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Installing Mesquite Packages<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Interactions with Other Programs.html b/docs/Interactions with Other Programs.html
index 9167a8f52..5f9151d30 100644
--- a/docs/Interactions with Other Programs.html	
+++ b/docs/Interactions with Other Programs.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Interactions with Other Programs<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Learning how to use Mesquite.html b/docs/Learning how to use Mesquite.html
index f106a84d3..6501c96b7 100644
--- a/docs/Learning how to use Mesquite.html	
+++ b/docs/Learning how to use Mesquite.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Learning Mesquite<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Managing Continuous Data.html b/docs/Managing Continuous Data.html
index b0ec75d30..4d40939f8 100644
--- a/docs/Managing Continuous Data.html	
+++ b/docs/Managing Continuous Data.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Managing Continuous Data<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Managing Molecular Data.html b/docs/Managing Molecular Data.html
index 9fc98d549..a80032314 100644
--- a/docs/Managing Molecular Data.html	
+++ b/docs/Managing Molecular Data.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Managing Molecular Data<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Menus.html b/docs/Menus.html
index 2d099bd53..c3cf4769b 100644
--- a/docs/Menus.html
+++ b/docs/Menus.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Menus<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/MesquiteLogSupport.html b/docs/MesquiteLogSupport.html
index 4adcb4d2c..3ceb8b462 100644
--- a/docs/MesquiteLogSupport.html
+++ b/docs/MesquiteLogSupport.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Log &amp; Support Files<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Mesquites Features.html b/docs/Mesquites Features.html
index 1b496bbd6..b10a75426 100644
--- a/docs/Mesquites Features.html	
+++ b/docs/Mesquites Features.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Mesquite's Features<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
@@ -200,7 +200,7 @@ <h3>&nbsp;</h3>
     
 <h1 id="toc0"><a name="List of Features"></a>List of Features</h1>
  Below is a brief outline of Mesquite features. Many of the links within the outline take you to screenshots, some of which show older versions of Mesquite. To see features recently added to Mesquite, see the manual page on <a  href="History%20of%20New%20Features.html">new features</a>. <br />
-<ul><li><a  href="Mesquite%27s%20Features.html#overview">Overview</a></li><li><a  href="Mesquite%27s%20Features.html#analyses">Analyses</a></li><li><a  href="Mesquite%27s%20Features.html#characters">Characters</a></li><li><a  href="Mesquite%27s%20Features.html#taxa">Taxa</a></li><li><a  href="Mesquite%27s%20Features.html#trees">Trees</a></li><li><a  href="Mesquite%27s%20Features.html#otherfeatures">Other features</a></li></ul><h2 id="toc1"><a name="List of Features-Overview"></a><a name="overview"></a>Overview</h2>
+<ul><li><a  href="#overview">Overview</a></li><li><a  href="#analyses">Analyses</a></li><li><a  href="#characters">Characters</a></li><li><a  href="#taxa">Taxa</a></li><li><a  href="#trees">Trees</a></li><li><a  href="#otherfeatures">Other features</a></li></ul><h2 id="toc1"><a name="List of Features-Overview"></a><a name="overview"></a>Overview</h2>
  Primary entities are taxa (which may represent species, genes, samples, and so on), characters (features or variables), and trees.<br />
 <ul><li>Files may contain:Files may be linked into projects<ul><li>Multiple matrices</li><li>Multiple taxa blocks</li><li>Multiple blocks of trees</li></ul></li><li><br />
 </li><li>Multiple files may be open simultaneously</li></ul><h2 id="toc2"><a name="List of Features-Analyses"></a><a name="analyses"></a>Analyses</h2>
diff --git a/docs/Module Index.html b/docs/Module Index.html
index 39c8c391a..5cd733040 100644
--- a/docs/Module Index.html	
+++ b/docs/Module Index.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Module Index<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Modules.html b/docs/Modules.html
index 8f2c2fc93..875a6dcd9 100644
--- a/docs/Modules.html
+++ b/docs/Modules.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Modules<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Pagel Correlation Method.html b/docs/Pagel Correlation Method.html
index 4967fd047..4f6eaec2b 100644
--- a/docs/Pagel Correlation Method.html	
+++ b/docs/Pagel Correlation Method.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Pagel Correlation Method<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Processes of Character Evolution.html b/docs/Processes of Character Evolution.html
index 676777edf..1eeb50e13 100644
--- a/docs/Processes of Character Evolution.html	
+++ b/docs/Processes of Character Evolution.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Processes of Character Evolution<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Publication Quality Trees.html b/docs/Publication Quality Trees.html
index 6f38c46e3..4bae4cdf2 100644
--- a/docs/Publication Quality Trees.html	
+++ b/docs/Publication Quality Trees.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Publication Quality Trees<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Publishing Results.html b/docs/Publishing Results.html
index 7a09d9d7b..d38342463 100644
--- a/docs/Publishing Results.html	
+++ b/docs/Publishing Results.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Publishing Results<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Release Dates.html b/docs/Release Dates.html
index 2e1875c3a..71da41444 100644
--- a/docs/Release Dates.html	
+++ b/docs/Release Dates.html	
@@ -217,6 +217,17 @@ <h1 id="toc0"><a name="Release Dates"></a><span style="background-color: #ffffff
 </td>
     </tr>
     <tr>
+        <td><strong>3.61</strong><br />
+</td>
+        <td><br />
+</td>
+        <td>927<br />
+</td>
+        <td><br />
+</td>
+        <td>26 December 2019<br />
+</td>
+    </tr>     <tr>
         <td><strong>3.6</strong><br />
 </td>
         <td><br />
diff --git a/docs/Scripts & Macros.html b/docs/Scripts & Macros.html
index 905192412..64438813c 100644
--- a/docs/Scripts & Macros.html	
+++ b/docs/Scripts & Macros.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Scripts &amp; Macros<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Simplifying the Interface.html b/docs/Simplifying the Interface.html
index 3f720f150..8e65e0ea4 100644
--- a/docs/Simplifying the Interface.html	
+++ b/docs/Simplifying the Interface.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Simplifying the Interface<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Simulating Characters.html b/docs/Simulating Characters.html
index 9fbe47aa8..9e124c651 100644
--- a/docs/Simulating Characters.html	
+++ b/docs/Simulating Characters.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Simulating Characters<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Simulating DNA Evolution.html b/docs/Simulating DNA Evolution.html
index 8e5e5fe79..96228580e 100644
--- a/docs/Simulating DNA Evolution.html	
+++ b/docs/Simulating DNA Evolution.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Simulating DNA Evolution<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Simulations & Randomizations.html b/docs/Simulations & Randomizations.html
index d6b311798..b1e163749 100644
--- a/docs/Simulations & Randomizations.html	
+++ b/docs/Simulations & Randomizations.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Simulations &amp; Randomizations<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Slatkin and Maddison.html b/docs/Slatkin and Maddison.html
index 3846368d0..65ecc29ff 100644
--- a/docs/Slatkin and Maddison.html	
+++ b/docs/Slatkin and Maddison.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Slatkin and Maddison<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Source Code.html b/docs/Source Code.html
index bd35d529a..d48974339 100644
--- a/docs/Source Code.html	
+++ b/docs/Source Code.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Source Code<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Studies of Tree Topology.html b/docs/Studies of Tree Topology.html
index 18a14c159..83911a0a8 100644
--- a/docs/Studies of Tree Topology.html	
+++ b/docs/Studies of Tree Topology.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Studies of Tree Topology<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Suggesting New Features.html b/docs/Suggesting New Features.html
index c143e42ab..5cdd51c2e 100644
--- a/docs/Suggesting New Features.html	
+++ b/docs/Suggesting New Features.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Suggesting New Features<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Taxa.html b/docs/Taxa.html
index 62833fdec..d62d2ffbe 100644
--- a/docs/Taxa.html
+++ b/docs/Taxa.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Taxa<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Templates/MesquiteTemplate.dwt b/docs/Templates/MesquiteTemplate.dwt
index 05212f503..75a4e7404 100644
--- a/docs/Templates/MesquiteTemplate.dwt
+++ b/docs/Templates/MesquiteTemplate.dwt
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- TemplateBeginEditable name="subtitle" -->subtitle<!-- TemplateEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Testing monophyly of a group of beetles.html b/docs/Testing monophyly of a group of beetles.html
index 538a74d03..6d3cb2310 100644
--- a/docs/Testing monophyly of a group of beetles.html	
+++ b/docs/Testing monophyly of a group of beetles.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Example: Testing monophyly<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Tree Simulations.html b/docs/Tree Simulations.html
index 62e5ba5e2..6bdaf73f0 100644
--- a/docs/Tree Simulations.html	
+++ b/docs/Tree Simulations.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Tree Simulations<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/Trees.html b/docs/Trees.html
index 50e5374e3..d762864b0 100644
--- a/docs/Trees.html
+++ b/docs/Trees.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Trees<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/What Mesquite does.html b/docs/What Mesquite does.html
index 6cce4218d..f484d7b44 100644
--- a/docs/What Mesquite does.html	
+++ b/docs/What Mesquite does.html	
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Introduction to Mesquite<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
@@ -200,7 +200,7 @@ <h3>&nbsp;</h3>
     
 <h1 id="toc0"><a name="What Mesquite Does"></a>What Mesquite Does</h1>
  <br />
-Mesquite is software for evolutionary biology, designed to help biologists manage and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses and management features available depend on the modules installed. Here is a brief overview of some of Mesquite's features. See also a more complete <a  href="Mesquite%27s%20Features.html">outline of features</a>, and the <span style="line-height: 1.5;"><a  href="http://www.youtube.com/channel/UCfSmgC0O_dWLI0PEoXZbS4Q" rel="nofollow">Mesquite Project Youtube channel</a>, with instructional videos helping you learn Mesquite.</span><br />
+Mesquite is software for evolutionary biology, designed to help biologists manage and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses and management features available depend on the modules installed. Here is a brief overview of some of Mesquite's features. See also a more complete <a  href="Mesquites%20Features.html">outline of features</a>, and the <span style="line-height: 1.5;"><a  href="http://www.youtube.com/channel/UCfSmgC0O_dWLI0PEoXZbS4Q" rel="nofollow">Mesquite Project Youtube channel</a>, with instructional videos helping you learn Mesquite.</span><br />
 <br />
 Despite Mesquite's broad <a  href="What%20Mesquite%20does.html#analysesExamples">analytical capabilities</a>, the developers of Mesquite find that we use Mesquite most often to provide a workflow of data editing, management, and processing. We will therefore begin there.<br />
 <br />
diff --git a/docs/Windows.html b/docs/Windows.html
index 986af42b7..24899bf63 100644
--- a/docs/Windows.html
+++ b/docs/Windows.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Windows<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
diff --git a/docs/home.html b/docs/home.html
index fbc0248db..11477f991 100644
--- a/docs/home.html
+++ b/docs/home.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" --><!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
@@ -198,7 +198,7 @@ <h3>&nbsp;</h3>
 <!-- InstanceBeginEditable name="content" --><br />
 <br />
 <h1 id="toc0"><a name="Mesquite: A modular system for evolutionary analysis"></a><span style="font-size: 130%;">Mesquite: A modular system for evolutionary analysis</span></h1>
- <h1 id="toc1"><a name="Current release version: 3.4 [download]"></a>Version: 3.6</h1>
+ <h1 id="toc1"><a name="Current release version: 3.4 [download]"></a>Version: 3.61</h1>
  <br />
 Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed.<br />
 <br />
diff --git a/docs/index.html b/docs/index.html
index 29da1b5c0..9cba99e2b 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Home<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
@@ -201,7 +201,7 @@ <h3>&nbsp;</h3>
 <em>If you're looking for Mesquite Software, Inc. or its CSIM toolkit for building simulation models, go <a  href="http://www.mesquite.com/" rel="nofollow">here</a></em><br />
 <br />
 <h1 id="toc0"><a name="Mesquite: A modular system for evolutionary analysis"></a><span style="font-size: 130%;">Mesquite: A modular system for evolutionary analysis</span></h1>
- <h1 id="toc1"><a name="Current release version: 3.4 [download]"></a>Current release version: 3.6 [<a  href="Installation.html">download</a>]</h1>
+ <h1 id="toc1"><a name="Current release version: 3.4 [download]"></a>Current release version: 3.61 [<a  href="Installation.html">download</a>]</h1>
  <p><em>If you have a previous version, please <a  href="Installation.html">update</a> because of <a  href="History%20of%20New%20Features.html">bug fixes and new features</a>.</em><br />
   <br />
    Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed.</p>
diff --git a/docs/noticesAndUpdates/notices.xml b/docs/noticesAndUpdates/notices.xml
index 209afe2f4..eaeb284d3 100644
--- a/docs/noticesAndUpdates/notices.xml
+++ b/docs/noticesAndUpdates/notices.xml
@@ -4,66 +4,74 @@
 	<MessagesFromHome>
 		<version>1</version>
 		<currentReleaseVersion>
-			<versionString>3.60</versionString>
-			<build>917</build>
-			<version>360</version>
+			<versionString>3.61</versionString>
+			<build>927</build>
+			<version>361</version>
 			<downloadURL>http://www.mesquiteproject.org/Installation.html</downloadURL>
 		</currentReleaseVersion>
+		<notice>
+			<forVersion>360</forVersion>
+			<noticeNumber>25</noticeNumber>
+			<messageType>alert</messageType>
+			<message><![CDATA[A new version of Mesquite is available, version 3.61, with various new features and bug fixes.  
+			We urge that you update to the new version by downloading it from 
+			<a href = "http://github.com/MesquiteProject/MesquiteCore/releases">here</a>]]></message>
+		</notice>
 		<notice>
 			<forVersion>351</forVersion>
-			<noticeNumber>24</noticeNumber>
+			<noticeNumber>25</noticeNumber>
 			<messageType>alert</messageType>
-			<message><![CDATA[A new version of Mesquite is available, version 3.6, with various new features and bug fixes.  
+			<message><![CDATA[A new version of Mesquite is available, version 3.61, with various new features and bug fixes.  
 			We urge that you update to the new version by downloading it from 
 			<a href = "http://github.com/MesquiteProject/MesquiteCore/releases">here</a>]]></message>
 		</notice>
 		<notice>
 			<forVersion>350</forVersion>
-			<noticeNumber>24</noticeNumber>
+			<noticeNumber>25</noticeNumber>
 			<messageType>alert</messageType>
-			<message><![CDATA[A new version of Mesquite is available, version 3.6, with various new features and bug fixes.  
+			<message><![CDATA[A new version of Mesquite is available, version 3.61, with various new features and bug fixes.  
 			We urge that you update to the new version by downloading it from 
 			<a href = "http://github.com/MesquiteProject/MesquiteCore/releases">here</a>]]></message>
 		</notice>
 		<notice>
 			<forVersion>340</forVersion>
-			<noticeNumber>24</noticeNumber>
+			<noticeNumber>25</noticeNumber>
 			<messageType>alert</messageType>
-			<message><![CDATA[A new version of Mesquite is available, version 3.6, with various new features and bug fixes, an offline manual and a new location for  
+			<message><![CDATA[A new version of Mesquite is available, version 3.61, with various new features and bug fixes, an offline manual and a new location for  
 			<a href = "http://www.mesquiteproject.org">the website</a>.  
 			We urge that you update to the new version by downloading it from 
 			<a href = "http://github.com/MesquiteProject/MesquiteCore/releases">here</a>]]></message>
 		</notice>
 		<notice>
 			<forVersion>331</forVersion>
-			<noticeNumber>24</noticeNumber>
+			<noticeNumber>25</noticeNumber>
 			<messageType>alert</messageType>
-			<message><![CDATA[YOU ARE USING AN OLD VERSION of Mesquite. Your version is no longer supported. A new version of Mesquite is available, version 3.6, with various new features and bug fixes, compatibility with Java 9, an offline manual and a new location for  
+			<message><![CDATA[YOU ARE USING AN OLD VERSION of Mesquite. Your version is no longer supported. A new version of Mesquite is available, version 3.61, with various new features and bug fixes, compatibility with Java 9, an offline manual and a new location for  
 			<a href = "http://www.mesquiteproject.org">the website</a>.  
 			We urge that you update to the new version by downloading it from 
 			<a href = "http://github.com/MesquiteProject/MesquiteCore/releases">here</a>]]></message>
 		</notice>
 		<notice>
 			<forVersion>330</forVersion>
-			<noticeNumber>24</noticeNumber>
+			<noticeNumber>25</noticeNumber>
 			<messageType>alert</messageType>
-			<message><![CDATA[YOU ARE USING AN OLD VERSION of Mesquite. Your version is no longer supported. A new version of Mesquite is available, version 3.6, with various new features and bug fixes, compatibility with Java 9, an offline manual and a new location for  
+			<message><![CDATA[YOU ARE USING AN OLD VERSION of Mesquite. Your version is no longer supported. A new version of Mesquite is available, version 3.61, with various new features and bug fixes, compatibility with Java 9, an offline manual and a new location for  
 			<a href = "http://www.mesquiteproject.org">the website</a>.  
 			We urge that you update to the new version by downloading it from 
 			<a href = "http://github.com/MesquiteProject/MesquiteCore/releases">here</a>]]></message>
 		</notice>
 		<notice>
 			<forMesquiteVersionLessOrEqual>330</forMesquiteVersionLessOrEqual>
-			<noticeNumber>24</noticeNumber>
+			<noticeNumber>25</noticeNumber>
 			<messageType>alert</messageType>
-			<message><![CDATA[YOU ARE USING A VERY OLD VERSION of Mesquite. Your version is no longer supported. A new version is available, version 3.6, with many new features and bug fixes, compatibility with Java 9, performance improvements, an offline manual and a new location for  
+			<message><![CDATA[YOU ARE USING A VERY OLD VERSION of Mesquite. Your version is no longer supported. A new version is available, version 3.61, with many new features and bug fixes, compatibility with Java 9, performance improvements, an offline manual and a new location for  
 			<a href = "http://www.mesquiteproject.org">the website</a>.  
 			We strongly urge that you update to the new version by downloading it from 
 			<a href = "http://github.com/MesquiteProject/MesquiteCore/releases">here</a>]]></message>
 		</notice>
 		<notice>
 			<forVersion>201</forVersion>
-			<noticeNumber>24</noticeNumber>
+			<noticeNumber>25</noticeNumber>
 			<messageType>alert</messageType>
 			<message>This notice is to inform you that Mesquite now checks its web site for notices to users (such as this one) when it starts up.  This should not cause a delay (if it does, please inform us).  We anticipate notices will be given rarely, when there is an update available or an important bug to tell you about.</message>
 		</notice>
diff --git a/docs/space.menu.html b/docs/space.menu.html
index ffe797996..284050eff 100644
--- a/docs/space.menu.html
+++ b/docs/space.menu.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" --><!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>
 
@@ -200,14 +200,14 @@ <h3>&nbsp;</h3>
     
 <h3><a  href="Mesquite.html">Mesquite Home Page</a></h3>
  <h3>Overview of Mesquite</h3>
- <ul><li><a  href="What%20Mesquite%20does.html">What Mesquite Does</a></li><li><a  href="Mesquite%27s%20Features.html">List of Features</a></li><li><a  href="History%20of%20New%20Features.html">Recent Changes</a></li><li><a  href="Development%20Team.html">Development Team</a></li><li><a  href="Contact%20Us.html">Contact Us</a></li></ul><h3>Getting Started</h3>
+ <ul><li><a  href="What%20Mesquite%20does.html">What Mesquite Does</a></li><li><a  href="Mesquites%20Features.html">List of Features</a></li><li><a  href="History%20of%20New%20Features.html">Recent Changes</a></li><li><a  href="Development%20Team.html">Development Team</a></li><li><a  href="Contact%20Us.html">Contact Us</a></li></ul><h3>Getting Started</h3>
  <ul><li><a  href="Installation.html">Download and Installation</a></li><li><a  href="Additional%20Mesquite%20Packages.html">Additional Packages</a></li><li><a  href="Beginning%20Mesquite.html">Beginning Mesquite</a></li><li><a  href="Example%20Files.html">Example Files</a></li></ul><h3>Basics</h3>
  <ul><li><a  href="Files.html">Files</a></li><li><a  href="Menus.html">Menus</a></li><li><a  href="Windows.html">Windows</a></li><li><a  href="Charts.html">Charts</a></li><li><a  href="Selection.html">Selection</a></li><li><a  href="Modules.html">Modules</a></li><li><a  href="Simplifying%20the%20Interface.html">Simplifying Mesquite</a></li></ul><h3>Objects</h3>
  <ul><li><a  href="Characters%20%26%20Matrices.html">Characters</a></li><li><a  href="Taxa.html">Taxa</a></li><li><a  href="Trees.html">Trees</a></li></ul><h3>Analyses</h3>
  <ul><li><a  href="Character%20Evolution.html">Character Evolution</a></li><li><a  href="Diversification.html">Diversification</a></li><li><a  href="Analyzing%20Molecular%20Data.html">Molecular Data</a></li><li><a  href="Gene%20Trees.html">Gene Trees</a></li><li><a  href="Simulations%20%26%20Randomizations.html">Simulations &amp; Randomizations</a></li><li><a  href="Analyzing%20Continuous%20Characters.html">Continuous Characters</a></li><li><a  href="Studies%20of%20Tree%20Topology.html">Studies of Tree Topology</a></li></ul><h3>Workflows</h3>
  <ul><li><a  href="Managing%20Molecular%20Data.html">Managing Molecular Data</a></li><li><a  href="Managing%20Continuous%20Data.html">Managing Continuous Data</a></li><li><a  href="Interactions%20with%20Other%20Programs.html">Interactions with other programs</a></li></ul><h3>Getting Help</h3>
  <ul><li><a  href="Learning%20how%20to%20use%20Mesquite.html">Learning Mesquite</a></li><li><a  href="Bugs%20and%20Troubleshooting.html">Bugs &amp; Troubleshooting</a></li><li><a  href="Getting%20Help.html">Getting Help</a></li><li><a  href="Suggesting%20New%20Features.html">Your Suggestions</a></li><li><a  href="Glossary.html">Glossary</a></li><li><a  href="FAQ.html">FAQ</a></li></ul><h3>Technical Details</h3>
- <ul><li><a  href="How%20Mesquite%20Works.html">How Mesquite Works</a></li><li><a  href="Scripts%20%26%20Macros.html">Scripts &amp; Macros</a></li><li><a  href="Source%20Code.html">Source Code</a></li><li><a  href="Developer%27s%20Documentation.html">Developer's Documentation</a></li></ul><h3>History</h3>
+ <ul><li><a  href="How%20Mesquite%20Works.html">How Mesquite Works</a></li><li><a  href="Scripts%20%26%20Macros.html">Scripts &amp; Macros</a></li><li><a  href="Source%20Code.html">Source Code</a></li><li><a  href="Developers%20Documentation.html">Developer's Documentation</a></li></ul><h3>History</h3>
  <ul><li><a  href="History%20of%20Mesquite.html">History of Mesquite</a></li><li><a  href="Why%3F.html">Why Mesquite?</a></li><li><a  href="History%20of%20New%20Features.html">New Features &amp; Bug List</a></li><li><a  href="Release%20Dates.html">Release Dates</a></li></ul><h3>Publishing Results</h3>
  <ul><li><a  href="Documenting%20Your%20Work.html">Documenting your work</a></li><li><a  href="How%20to%20Cite%20Mesquite.html">Citing Mesquite</a></li><li><a  href="Publishing%20Results.html">Publishing results</a></li></ul><h3><a  href="Acknowledgements.html">Acknowledgements</a></h3>
 <!-- InstanceEndEditable -->
diff --git a/docs/whyMesquite.html b/docs/whyMesquite.html
index bd4b8056f..dc0e1cf07 100644
--- a/docs/whyMesquite.html
+++ b/docs/whyMesquite.html
@@ -41,8 +41,8 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Why Mesquite?<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.6<br />
-      27 December 2018<br /></td>
+    <td width="14%">Version 3.61<br />
+      26 December 2019<br /></td>
   </tr>
 </table>