phylogenetics
There are 536 repositories under phylogenetics topic.
biopython/biopython
Official git repository for Biopython (originally converted from CVS)
etetoolkit/ete
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.
Ecogenomics/GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
amkozlov/raxml-ng
RAxML Next Generation: faster, easier-to-use and more flexible
edgardomortiz/vcf2phylip
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
CompEvol/beast2
Bayesian Evolutionary Analysis by Sampling Trees
NBISweden/MrBayes
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:
neherlab/treetime
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
veg/hyphy
HyPhy: Hypothesis testing using Phylogenies
KlausVigo/phangorn
Phylogenetic analysis in R
Cibiv/IQ-TREE
Efficient phylogenomic software by maximum likelihood
beast-dev/beast-mcmc
Bayesian Evolutionary Analysis Sampling Trees
stephaneguindon/phyml
PhyML -- Phylogenetic estimation using (Maximum) Likelihood
tskit-dev/tskit
Population-scale genomics
biologyguy/BuddySuite
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
yatisht/usher
Ultrafast Sample Placement on Existing Trees
hahnlab/CAFE
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
FePhyFoFum/phyx
phylogenetics tools for linux (and other mostly posix compliant) computers
hahnlab/CAFE5
Version 5 of the CAFE phylogenetics software
cogent3/cogent3
Comparative Genomics Toolkit 3
theosanderson/taxonium
A tool for exploring very large trees in the browser
evogytis/baltic
baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).
ODiogoSilva/TriFusion
Streamlining phylogenomic data gathering, processing and visualization
CDCgov/MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
Zsailer/phylopandas
Pandas DataFrames for phylogenetics
pierrebarbera/epa-ng
Massively parallel phylogenetic placement of genetic sequences
lczech/gappa
A toolkit for analyzing and visualizing phylogenetic (placement) data
lczech/genesis
A library for working with phylogenetic and population genetic data.
moshi4/ANIclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes
JLSteenwyk/ClipKIT
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
JLSteenwyk/PhyKIT
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
yangwu91/r2g
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
vinuesa/get_phylomarkers
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
lh3/jstreeview
Interactive phylogenetic tree viewer/editor
ropensci/babette
babette is an R package to work with BEAST2
nextstrain/mpox
Nextstrain build for mpox virus