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

Comparative Genomics Toolkit 3

Ultrafast Sample Placement on Existing Trees

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.