Official git repository for Biopython (originally converted from CVS)
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Updated
Jun 2, 2024 - Python
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.
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
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:
A course in the theory and practice of phylogenetic inference from DNA sequence data
Bayesian Evolutionary Analysis Sampling Trees
Population-scale genomics
HyPhy: Hypothesis testing using Phylogenies
RAxML Next Generation: faster, easier-to-use and more flexible
PhyML -- Phylogenetic estimation using (Maximum) Likelihood
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
Comparative Genomics Toolkit 3
Efficient phylogenomic software by maximum likelihood
Ultrafast Sample Placement on Existing Trees
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
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