phylogenetics

There are 20 repositories under phylogenetics topic.

• biopython / biopython

  Official git repository for Biopython (originally converted from CVS)

  pythonbioinformaticsgenomicsbiopythonproteinprotein-structuresequence-alignmentphylogeneticsdna
  Language:Python 4159

• 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.

  phylogeneticsphylogenomicpythontree-structuretreeviewvisualization
  Language:Python 751
• GTDBTk

  Ecogenomics / GTDBTk

  GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

  taxonomyspecies-assignmentsphylogeneticsarchaeabacterianomenclaturebioinformaticsmetagenomics
  Language:Python 426

• amkozlov / raxml-ng

  RAxML Next Generation: faster, easier-to-use and more flexible

  bioinformaticsphylogeneticsmaximum-likelihoodmpipthreads
  Language:C++ 356

• edgardomortiz / vcf2phylip

  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

  vcfsnpsphylipalignmentphylogeneticsnexusbinarysnappfastaoutgroupconvert-snpsvcf-filesphylogenetic-analysisvcf-formatphylip-matrixhaploiddiploidpolyploid
  Language:Python 249

• CompEvol / beast2

  Bayesian Evolutionary Analysis by Sampling Trees

  phylogeneticsbayesian-inferencemcmcbeastjavaevolution
  Language:Java 230

• 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:

  phylogeneticsbayesian-inferencemarkov-chain-monte-carloresearch-toolbioinformatics
  Language:C 218

• neherlab / treetime

  Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

  phylogenetics
  Language:Jupyter Notebook 204

• KlausVigo / phangorn

  Phylogenetic analysis in R

  rphylogenetic-analysisphylogenetics
  Language:R 196

• veg / hyphy

  HyPhy: Hypothesis testing using Phylogenies

  sciencebioinfomaticsphylogeneticsc-plus-plus
  Language:HyPhy 194

• Cibiv / IQ-TREE

  Efficient phylogenomic software by maximum likelihood

  maximum-likelihoodphylogenomicsphylogeneticsmixture-modeliq-treeultrafast-bootstrapmodel-selection
  Language:C++ 181

• beast-dev / beast-mcmc

  Bayesian Evolutionary Analysis Sampling Trees

  beastjavabayesian-analysismcmcphylogeneticsevolution
  Language:Java 176

• stephaneguindon / phyml

  PhyML -- Phylogenetic estimation using (Maximum) Likelihood

  mcmcphylogeneticsevolution
  Language:C 166
• tskit

  tskit-dev / tskit

  Population-scale genomics

  bioinformaticsgenomicsphylogeneticspythonsciencetree-sequences
  Language:Python 139

• biologyguy / BuddySuite

  Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

  bioinformaticspythonphylogeneticsdnaproteinalignmentcommand-lineworkflowbiology
  Language:Python 121
• usher

  yatisht / usher

  Ultrafast Sample Placement on Existing Trees

  sars-cov-2phylogeneticsmaximum-parsimonyushergenome-browserphylogenetic-placement
  Language:C++ 117

• hahnlab / CAFE

  Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

  gene-familiesbioinformaticsphylogenetics
  Language:C++ 108

• FePhyFoFum / phyx

  phylogenetics tools for linux (and other mostly posix compliant) computers

  phylogeneticsmolecular-evolutionsimulation
  Language:C++ 104

• hahnlab / CAFE5

  Version 5 of the CAFE phylogenetics software

  gene-familyphylogeneticsbioinformatics
  Language:C++ 101

• cogent3 / cogent3

  Comparative Genomics Toolkit 3

  bioinformaticspycogentstatisticsdata-sciencebiologygenomicsevolutionbiopythonmarkov-chainmolecular-evolutionnon-stationaryphylogenetic-treesphylogeneticspythonparallelsignal-processingmaximum-likelihoodbiological-sequence-analysissequence-alignment
  Language:Python 93

• theosanderson / taxonium

  A tool for exploring very large trees in the browser

  phylogeneticsphylogenytreedeckglreactvirus
  Language:JavaScript 89

• ODiogoSilva / TriFusion

  Streamlining phylogenomic data gathering, processing and visualization

  pythonphylogeneticsphylogenomicgeneticsorthologuesguikivyvisualization
  Language:Python 87

• 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).

  visualisationphylogenetics
  Language:Python 86
• MicrobeTrace

  CDCgov / MicrobeTrace

  The Visualization Multitool for Molecular Epidemiology and Bioinformatics

  bioinformaticsepidemiologynetwork-visualizationhivcdcpathogensphylogeneticsphylogenetic-treesphylogenyphylogenomicsgenomicsgenomics-visualizationgenomic-data-analysissequence-alignment
  Language:TypeScript 83

• Zsailer / phylopandas

  Pandas DataFrames for phylogenetics

  phylogeneticspythonpandasbiopython
  Language:Python 69

• pierrebarbera / epa-ng

  Massively parallel phylogenetic placement of genetic sequences

  phylogeneticsbioinformaticstaxonomic-classificationmpiopenmpmpi-ioplacement
  Language:C++ 66

• lczech / gappa

  A toolkit for analyzing and visualizing phylogenetic (placement) data

  c-plus-plusphylogeneticsphylogenetic-dataphylogenetic-placementevolutionary-placementplacementgenesisgappa
  Language:C++ 57

• lczech / genesis

  A library for working with phylogenetic and population genetic data.

  c-plus-plusphylogeneticsevolutionary-placementphylogenetic-dataphylogenetic-treesphylogenetic-placementsplacementpopulation-geneticspool-sequencing
  Language:C++ 56
• ClipKIT

  JLSteenwyk / ClipKIT

  a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

  bioinformaticsevolutionevolutionary-biologygenomicsphylogeneticsphylogenomicspythonsystematics
  Language:Python 52
• ANIclustermap

  moshi4 / ANIclustermap

  A tool for drawing ANI clustermap between all-vs-all microbial genomes

  pythonbioinformaticsgenomicsphylogeneticsphylogenomicsvisualizationcomparative-genomicstaxonomymicrobial-genomics
  Language:Python 52
• r2g

  yangwu91 / r2g

  A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly

  bioinformaticsncbi-srahomologyorthologybioinformatics-pipelinephylogeneticsgene-sequence-retrieval
  Language:Python 49
• PhyKIT

  JLSteenwyk / PhyKIT

  a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

  bioinformaticsevolutionevolutionary-biologygenomicsphylogeneticsphylogenomicspythonmultiple-sequence-alignments
  Language:Python 47

• lh3 / jstreeview

  Interactive phylogenetic tree viewer/editor

  bioinformaticsphylogenetics
  Language:JavaScript 46

• vinuesa / get_phylomarkers

  A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

  phylogenomicspopulation-geneticsphylogenomics-pipelinespecies-treesmarkersgenomicspipelinephylogeneticsphylogenetic-treescodon-alignmentmaximum-likelihoodorthologuesspecies-delimitationmicrobiologycore-genomeperlrbashclock-hypothesisrecombination
  Language:Perl 46

• ropensci / babette

  babette is an R package to work with BEAST2

  rr-packagerstatsphylogeneticsbeast2bayesian-inference
  Language:R 41

• nextstrain / mpox

  Nextstrain build for mpox virus

  monkeypoxphylogeneticsaugurauspicebioinformaticsgenbankgenomic-epidemiologymetadatanextstrainpipelinevirus-evolutionmpox
  Language:Python 39