forester
forester: software libraries for evolutionary biology and comparative genomics research
Overview
forester is a collection of open source libraries of Java, Ruby, and JavaScript software for phylogenomics and evolutionary biology research. For example, the tree viewer Archaeopteryx is based on forester.
The current developer version is available at GitHub at: https://github.com/cmzmasek/forester
Documentation and examples (under development): forester wiki
Applications
Archaeopteryx evolutionary tree explorer (desktop)
Archaeopteryx.js evolutionary tree explorer (online)
cladinator analysis of hierarchically annotated phylogenetic trees
rid sequence file reformatting and identifier normalization
msa_compactor post-processing of multiple sequence alignments
GSDI generalized speciation duplication inference
RIO resampled inference of orthologs
confadd calculation of typed confidence values for a given evolutionary tree
pccx phylogeny based target selection for structural genomics (experimental)