[BioRuby] [GSoC] Progress Update

Sara Rayburn sararayburn at gmail.com
Sun Jul 25 03:55:10 UTC 2010


Here is an update on the status of my project implementing speciation/duplication inference algorithms for BioRuby. The SDI algorithm is implemented, tested, and working for binary gene and species trees. This week I've ironed out some performance bottlenecks so that the algorithm executes almost as quickly as the Java implementation for very large trees. I have also completed the implementation of an extension to the algorithm that finds the gene tree rooting that minimizes the number of duplications inferred in the tree. Upcoming work will include extending the algorithm to support trees with more than two children per node. For more details, a full update is on the github wiki[1] for my branch along with a tutorial describing how to use the algorithms. 

[1] http://wiki.githubcom/srayburn/bioruby/


Sara Rayburn

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