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Top 27 phylogenetics open source projects

archaeopteryx-js
Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.
PCG
𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search
CAFE5
Version 5 of the CAFE phylogenetics software
phylogenetics-class
A course in the theory and practice of phylogenetic inference from DNA sequence data
phyml
PhyML -- Phylogenetic estimation using (Maximum) Likelihood
pastml
Ancestor character reconstruction and visualisation for rooted phylogenetic trees
BuddySuite
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
baltic
baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).
RNeXML
Implementing semantically rich NeXML I/O in R
SubstitutionModels.jl
Biological Sequence Substitution Models for Julia
booster
booster.c3bi.pasteur.fr
r2g
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
q2-qemistree
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
phylonium
♥ Fast and Accurate Estimation of Evolutionary Distances
TreeSAPP
A Python package for gene-centric taxonomic and functional classification using phylogenetic placement
CAFE
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
taxonium
A tool for exploring very large trees in the browser
1-27 of 27 phylogenetics projects