BiopythonOfficial git repository for Biopython (originally converted from CVS)
libpllPhylogenetic Likelihood Library
archaeopteryx-jsArchaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.
PCG𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search
CAFE5Version 5 of the CAFE phylogenetics software
genesisA library for working with phylogenetic and population genetic data.
phylogenetics-classA course in the theory and practice of phylogenetic inference from DNA sequence data
phymlPhyML -- Phylogenetic estimation using (Maximum) Likelihood
pastmlAncestor character reconstruction and visualisation for rooted phylogenetic trees
BuddySuiteBioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
get phylomarkersA pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches
balticbaltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).
RNeXMLImplementing semantically rich NeXML I/O in R
r2gA homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
q2-qemistreeHierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
usherUltrafast Sample Placement on Existing Trees
stsSequential Tree Sampler for online phylogenetics
phylonium♥ Fast and Accurate Estimation of Evolutionary Distances
TreeSAPPA Python package for gene-centric taxonomic and functional classification using phylogenetic placement
CAFEAnalyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
taxoniumA tool for exploring very large trees in the browser
FAVITESFAVITES (FrAmework for VIral Transmission and Evolution Simulation)