forester: software libraries for evolutionary biology and comparative genomics research

Overview

forester is a collection of open source libraries of JavaRuby, 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
  • phyloxml converter
  • phylogeny decorator
  • confadd calculation of typed confidence values for a given evolutionary tree
  • pccx phylogeny based target selection for structural genomics (experimental)
  • surfacing functional analysis of genome/domainome evolution (experimental)