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
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
Ultrafast Sample Placement on Existing Trees
Version 5 of the CAFE phylogenetics software
Comparative Genomics Toolkit 3
phylogenetics tools for linux (and other mostly posix compliant) computers
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
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