forester | software libraries for evolutionary biology and comparative genomics research


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 Google code at:

Documentation and examples (under development): forester wiki


Archaeopteryx — evolutionary tree explorer (successor to ATV)

goac — gene ontology (GO) ancestor term counting

phyloxml converter

phylogeny decorator

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

surfacing — functional analysis of genome/domainome evolution


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Last updated 08. Jan. 2009 | phyloxml