Please add your user cases below:

• Tree manipulation use cases (Suggested by Brian O'Meara and Val Tannen)
  • Tree subsetting
    Starting with some larger tree (either the eventual Plant ToL that iPToL will produce, or earlier approximations or some other tree from sources like Phylota or Treebase, or a user-supplied tree) the system is directed to select a portion of it and produce a smaller tree. This may happen in several incremental steps so the following operations will start from some tree and produce another, which may be subject to further selection, etc.
    1. Given a tree T and an internal node N in T output the subtree (the clade) of T rooted at N. This includes all the leaves in T descended from N.To use this functionality, the user must be able to specify internal nodes (see below).
    2. Given a tree T and a set S of leaves in T output a pruned tree whose root is the _most recent common ancestor_ (MRCA) of the leaves in S and whose leaves are exactly the leaves in S. This entails deleting all the branches leading to the other leaves. Nodes with just one descendant and ancestor (nodes with degree 2) are identified and deleted, merging their ancestor and descendant branches
• Details...

• Use cases from Tree Visualization group

• Possible Use Cases for a TR Discovery Environment

• Use Cases for Tree Reconciliation prototype