Working with tree collections

A collection is a curated ordered list of trees. Any user can create a collection, add / delete trees to a collection, or modify the order. Collections are stored on github, which means that we have a full history of additions, deletions, and changes to any collection. You will need a GitHub account to start. See OpenTree user accounts and GitHub for more information about setting up your account and why we use GitHub.

We use collections to manage the inputs to synthesis. At this point, there isn't much other functionality built into the web application for collections, but that is something that we are working on. Possibilities include custom synthesis, conflict statistics, or other analyses. Have a suggestion? Leave a new issue in the feedback repo.

You can browse the full list of collections on the collections page.

• Adding a new collection
• Editing collections
  • Adding trees from the collection window
  • [Adding trees from the study curator](#adding trees from the study curator)
• Adding trees to synthesis

Adding a new collection

To create a new collection, click the in any of these three places:

• from the list of collections (menu Tree collections->Browser all collections)
• from your curator profile page (menu Tree collections->Manage my collections
• from the Collections tab when viewing / editing a tree

Then, enter a name and a description for the collection. Click Save.

Editing collections

Click on any collection to open the collection window.

Click the blue Edit button to change to edit mode. On this window, you can:

• edit the comment for any tree
• click the red X to the right of any tree to delete it from the collection (this does not delete the tree)
• change the order of the trees using the Up and Down arrows, or by editing the rank number directly

You can add trees from the collections window ('add tree X to this collection'), or from a study ('add this tree to collection X').

Adding trees from the collections window

Click Add tree to this collection, at the bottom of the window to open up the add tree fields:

Enter either the studyID and treeID or the URL to the tree (you can get either one from the curator application). Note that the studyID includes the prefix (e.g. ot_234 or pg_264) and the tree ID may include tree at the start. Once you have entered the fields, click the blue plus button. A message at the bottom of the browser window will indicate if the tree has been added successfully or if there was an error.

Adding trees from the study curator

On the Trees tab, click on any tree to open the tree browser. Then, select the Collections tab. Click the appropriate button to add the tree to an existing collection or to create a new collection with this tree. When adding to an existing collection, use the search box to find the collection based on curator, name, ID, etc.

Adding trees to synthesis

The Inputs to synthesis collections are the lists of trees currently used to create the synthetic tree. If you want to include a tree in synthesis, add it to the appropriate collection. You can also rank the tree in the list, which will make it override conflicts from lower-ranked trees. Note that all trees in the default synthesis collection are always going to be lower-ranked than any of the taxon-based collections.