Official git repository for Biopython (originally converted from CVS)
Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCB...
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
RAxML Next Generation: faster, easier-to-use and more flexible
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
Bayesian Evolutionary Analysis by Sampling Trees
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
HyPhy: Hypothesis testing using Phylogenies
Bayesian Evolutionary Analysis Sampling Trees
PhyML -- Phylogenetic estimation using (Maximum) Likelihood
Population-scale Ancestral Recombination Graph (ARG) library
Comparative Genomics Toolkit 3
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
phylogenetics tools for linux (and other mostly posix compliant) computers
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.