phylogenetics

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 NCBI taxonomy tree.

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

Phylogenetic analysis in R

Efficient phylogenomic software by maximum likelihood

PhyML -- Phylogenetic estimation using (Maximum) Likelihood

Population-scale Ancestral Recombination Graph (ARG) library

Version 5 of the CAFE phylogenetics software

Ultrafast Sample Placement on Existing Trees

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.