Requirements

• Python 3.7

Packages Used

• dendropy
• Bio
• scipy
• numpy
• argparse

FP measures in the tool

The statistic arguments are as follows:

• fpmin: minimum FP
• fpmax: maximum FP

Tutorial

To run this tool on a nexus tree please follow the steps below:

1. place a nexus binary treefile in the same directory as the project
2. run FP.py with the following arguements: treename, (int)k, function (-fpmin,-fpmax)

• example : FP.py t10.tre 3 -fpmax The example above runs FP on the example treefile with 10 taxa and finds the 3 taxa with max fp in the tree.

  Note: the user can run multiple functions on the treefile, eg. pdstat.py treename.tre 10 -fpmax -fpmin

3. The output of the above command will be a file named "annotated_tree_nex" with all the the terminal clades annotated with their FP indec . This tree file can be opened with FigTree, and the nodes annotated using the "node labels" or "node shapes" menu. In addition, -fpmax returns max_list.txt i.e a txt file with the k max fp node names and values. The same is done for -fpmin with min_list.txt

Input test files with different numbers of input taxa are also present in the Test_Datasets directory