forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research. For example, the tree viewer Archaeopteryx is based on forester.
The current developer version is available through SourceForge's CVS at: http://sourceforge.net/projects/forester-atv/
Archaeopteryx — evolutionary tree explorer (successor to ATV)
goac — gene ontology (GO) ancestor term counting
confadd — calculation of typed confidence values for a given evolutionary tree
pccx — phylogeny based target selection for structural genomics
SDI — speciation duplication inference
SDI R — speciation duplication inference on unrooted trees
RIO — resampled inference of orthologs
Christian M Zmasek
Burnham Institute for Medical Research | cmzmasek yahoo com
Last updated 08. Jan. 2009