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
Efficient phylogenomic software by maximum likelihood
PhyML -- Phylogenetic estimation using (Maximum) Likelihood
Population-scale genomics
Ultrafast Sample Placement on Existing Trees
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
Version 5 of the CAFE phylogenetics software
phylogenetics tools for linux (and other mostly posix compliant) computers
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
Comparative Genomics Toolkit 3
Add a description, image, and links to the phylogenetics topic page so that developers can more easily learn about it.
To associate your repository with the phylogenetics topic, visit your repo's landing page and select "manage topics."