Prototype Development Discussion

Owned by Former user (Deleted)
Last updated: Jan 20, 2010Version comment
1 min read

I went through some of the Notung's "intro" materials and a few "Worked Examples". Some assumptions I wanted to ensure I correct:

Assumption

from my experience at tolweb, a non-binary tree is one containing polytomies. And a binary tree is a fully-resolved tree only representing branching events. (I'm quite confident about this, but just want to check).

Some questions:

  • are trees containing polytomies trouble for TreeBeST? Will we need to do some pre-processing to determine if there input trees are valid?
  • does TreeBeST require any "special" naming of the terminals in order to maintain a mapping from the species in the species tree and the genes in the gene tree? (I noticed that Notung requires a substring in the naming to determine which gene is related to which species)
  • (In the Discovery Environment) are we going to need a way to identify that a species tree from a gene tree?