Prototype Development Discussion
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?