[BioRuby] [GSoC] final project status

[Sara Rayburn]

Hi everyone,

Well, GSoC is finished for this summer. Thanks for a great experience working with Bioruby (especially thanks to Christian and Diana for mentoring). It's been a fun and challenging experience and I'm looking forward to continuing to work on the project beyond the scope of GSoC. Here's a quick rundown of the final status of my project:

-- The speciation/duplication inference algorithm is implemented in Bio::Algorithm::SDI for fully binary gene & species trees. There is also an alternative algorithm that will reroot the gene tree to minimize the number of duplicaitons. This is in Bio::Algorithm::SDIR. The more generalized algorithm is implemented in Bio::Algorithm::GSDI, but is unverified and not recommended for general use yet. 

There are things that i'd like to further work on, including refactoring some of the code and improving my unit tests. Also, I'm going to continue working on verifying the generalized algorithm.

Again, thanks for a great summer and a great opportunity!

Sara Rayburn