Official git repository for Biopython (originally converted from CVS)
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
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:
HyPhy: Hypothesis testing using Phylogenies
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
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
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