[BioRuby] Gene duplications GSoC project: answers to some of your questions

[Christian M Zmasek]

Hi, Sara:

Regarding some of your questions posted on 
http://wiki.github.com/srayburn/bioruby/gsoc-2010-implementing-sdi-project-updates

Re: "Right now initialization loads from a hard coded file. I need to 
make this flexible so that trees can come from any file or from a 
previously loaded tree object":

The input of the algoruthm(s) should be tree-objects, reading the trees 
should not be part of the algorithm implementation.

Clearly, for testing you need to read the trees from files, but this 
should be implemented in your test code, not as part of the algorithm 
implementation itself.

Re: "The names of leaf nodes: how standard are they? Is there a standard 
format here? I’m going to look at example trees from the forester 
implementation to get ideas about this. If I’m still stumped I’ll check 
with my mentors."

No there is no standard. The only question for the purpose of this 
algorithm do they match or not. I.e. they names could just numbers, 
common names, or scientific names.

Hope this helps,

Christian