Topic: "phylogenetics"
biopython/biopython
Official git repository for Biopython (originally converted from CVS)
Language: Python - Size: 70.3 MB - Last synced at: 6 days ago - Pushed at: 20 days ago - Stars: 4,713 - Forks: 1,831
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.
Language: Python - Size: 127 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 843 - Forks: 222
Ecogenomics/GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Language: Python - Size: 29 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 541 - Forks: 90
amkozlov/raxml-ng
RAxML Next Generation: faster, easier-to-use and more flexible
Language: C++ - Size: 1.55 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 435 - Forks: 64
CompEvol/beast2
Bayesian Evolutionary Analysis by Sampling Trees
Language: Java - Size: 93.8 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 255 - Forks: 85
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:
Language: C - Size: 43.5 MB - Last synced at: 3 days ago - Pushed at: 5 months ago - Stars: 249 - Forks: 82
neherlab/treetime
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
Language: Jupyter Notebook - Size: 18.2 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 244 - Forks: 59
veg/hyphy
HyPhy: Hypothesis testing using Phylogenies
Language: HyPhy - Size: 57.9 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 239 - Forks: 69
edgardomortiz/vcf2phylip
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
Language: Python - Size: 136 KB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 232 - Forks: 80
beast-dev/beast-mcmc
Bayesian Evolutionary Analysis Sampling Trees
Language: Java - Size: 201 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 227 - Forks: 79
KlausVigo/phangorn
Phylogenetic analysis in R
Language: R - Size: 136 MB - Last synced at: 2 days ago - Pushed at: 10 days ago - Stars: 209 - Forks: 41
stephaneguindon/phyml
PhyML -- Phylogenetic estimation using (Maximum) Likelihood
Language: C - Size: 71.4 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 183 - Forks: 63
Cibiv/IQ-TREE 📦
Efficient phylogenomic software by maximum likelihood
Language: C++ - Size: 65.4 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 180 - Forks: 45
tskit-dev/tskit
Population-scale Ancestral Recombination Graph (ARG) library
Language: Python - Size: 18.9 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 169 - Forks: 77
hahnlab/CAFE5
Version 5 of the CAFE phylogenetics software
Language: C++ - Size: 3.13 MB - Last synced at: 6 days ago - Pushed at: 7 months ago - Stars: 144 - Forks: 25
yatisht/usher
Ultrafast Sample Placement on Existing Trees
Language: C++ - Size: 41.3 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 133 - Forks: 47
cogent3/cogent3
Comparative Genomics Toolkit 3
Language: Python - Size: 46.3 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 132 - Forks: 64
biologyguy/BuddySuite
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
Language: Python - Size: 269 MB - Last synced at: 22 days ago - Pushed at: almost 4 years ago - Stars: 127 - Forks: 23
FePhyFoFum/phyx
phylogenetics tools for linux (and other mostly posix compliant) computers
Language: C++ - Size: 57.7 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 117 - Forks: 17
hahnlab/CAFE
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
Language: C++ - Size: 14.2 MB - Last synced at: 6 days ago - Pushed at: over 4 years ago - Stars: 117 - Forks: 37
theosanderson/taxonium
A tool for exploring large trees in the browser
Language: TypeScript - Size: 260 MB - Last synced at: 2 days ago - Pushed at: 12 days ago - Stars: 114 - Forks: 22
husonlab/splitstree6
SplitsTree App
Language: Java - Size: 239 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 113 - Forks: 7
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).
Language: Python - Size: 34.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 107 - Forks: 31
CDCgov/MicrobeTrace Fork of AABoyles/MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
Language: TypeScript - Size: 216 MB - Last synced at: 9 days ago - Pushed at: 17 days ago - Stars: 94 - Forks: 42
ODiogoSilva/TriFusion
Streamlining phylogenomic data gathering, processing and visualization
Language: Python - Size: 100 MB - Last synced at: 14 days ago - Pushed at: almost 7 years ago - Stars: 89 - Forks: 23
moshi4/ANIclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes
Language: Python - Size: 184 MB - Last synced at: 2 days ago - Pushed at: 4 months ago - Stars: 85 - Forks: 10
pierrebarbera/epa-ng
Massively parallel phylogenetic placement of genetic sequences
Language: C++ - Size: 32.5 MB - Last synced at: 5 months ago - Pushed at: about 3 years ago - Stars: 82 - Forks: 8
JLSteenwyk/ClipKIT
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
Language: Python - Size: 25.9 MB - Last synced at: 30 days ago - Pushed at: 30 days ago - Stars: 77 - Forks: 5
steineggerlab/unicore
Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5
Language: Rust - Size: 482 KB - Last synced at: 2 days ago - Pushed at: 3 months ago - Stars: 74 - Forks: 9
Zsailer/phylopandas
Pandas DataFrames for phylogenetics
Language: Python - Size: 982 KB - Last synced at: 14 days ago - Pushed at: over 4 years ago - Stars: 74 - Forks: 21
JLSteenwyk/PhyKIT
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
Language: Python - Size: 17.5 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 73 - Forks: 8
lczech/genesis
A library for working with phylogenetic and population genetic data.
Language: C++ - Size: 17.4 MB - Last synced at: 1 day ago - Pushed at: 17 days ago - Stars: 65 - Forks: 12
jamiemcg/BUSCO_phylogenomics
BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins
Language: Python - Size: 347 KB - Last synced at: 5 months ago - Pushed at: 11 months ago - Stars: 64 - Forks: 9
lczech/gappa
A toolkit for analyzing and visualizing phylogenetic placement data
Language: C++ - Size: 11.3 MB - Last synced at: 3 days ago - Pushed at: 7 months ago - Stars: 63 - Forks: 7
vinuesa/get_phylomarkers
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
Language: Perl - Size: 115 MB - Last synced at: 4 months ago - Pushed at: 8 months ago - Stars: 55 - Forks: 9
nextstrain/mpox
Nextstrain build for mpox virus
Language: Python - Size: 30.6 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 50 - Forks: 23
yangwu91/r2g
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
Language: Python - Size: 29 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 48 - Forks: 2
ropensci/babette
babette is an R package to work with BEAST2
Language: R - Size: 10.2 MB - Last synced at: 3 days ago - Pushed at: 17 days ago - Stars: 46 - Forks: 6
lh3/jstreeview
Interactive phylogenetic tree viewer/editor
Language: JavaScript - Size: 31.3 KB - Last synced at: 4 months ago - Pushed at: about 2 years ago - Stars: 46 - Forks: 3
cmzmasek/archaeopteryx-js
Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.
Language: JavaScript - Size: 7.29 MB - Last synced at: 30 days ago - Pushed at: 2 months ago - Stars: 41 - Forks: 14
harmslab/topiary
Python framework for doing ancestral sequence reconstruction
Language: Python - Size: 60.9 MB - Last synced at: 6 days ago - Pushed at: about 1 year ago - Stars: 41 - Forks: 7
SysBioChalmers/HGTphyloDetect
HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.
Language: Python - Size: 7.68 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 40 - Forks: 6
albertyw/itolapi
Python API for the Interactive Tree of Life (iTOL)
Language: Python - Size: 682 KB - Last synced at: 6 days ago - Pushed at: 23 days ago - Stars: 39 - Forks: 11
niemasd/FAVITES
FAVITES (FrAmework for VIral Transmission and Evolution Simulation)
Language: Python - Size: 25.3 MB - Last synced at: 6 months ago - Pushed at: almost 2 years ago - Stars: 38 - Forks: 4
tgvaughan/icytree
Browser-based utility for phylogenetic tree visualisation.
Language: JavaScript - Size: 2.92 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 38 - Forks: 2
cmzmasek/forester
forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research
Language: Java - Size: 152 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 36 - Forks: 16
EcoJulia/Phylo.jl
Simple phylogenetic trees in Julia to work with Diversity.jl - https://github.com/EcoJulia/Diversity.jl
Language: Julia - Size: 14.2 MB - Last synced at: 3 days ago - Pushed at: 9 months ago - Stars: 36 - Forks: 13
evolbioinfo/pastml
Ancestral character reconstruction and visualisation for rooted phylogenetic trees
Language: Python - Size: 35.9 MB - Last synced at: 5 days ago - Pushed at: 3 months ago - Stars: 35 - Forks: 6
steineggerlab/ufcg
UFCG: Universal Fungal Core Genes
Language: Java - Size: 71.1 MB - Last synced at: 2 days ago - Pushed at: about 1 month ago - Stars: 33 - Forks: 0
TurakhiaLab/ROADIES
Tool for fully-automated inference of species trees from raw genome assemblies
Language: Python - Size: 279 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 33 - Forks: 3
JLSteenwyk/orthofisher
a broadly applicable tool for automated gene identification and retrieval
Language: Python - Size: 81.9 MB - Last synced at: 2 days ago - Pushed at: 9 months ago - Stars: 32 - Forks: 1
moshi4/CafePlotter
A tool for plotting CAFE5 gene family expansion/contraction result
Language: Python - Size: 3.77 MB - Last synced at: 7 days ago - Pushed at: almost 2 years ago - Stars: 32 - Forks: 3
biocore/q2-qemistree
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
Language: Python - Size: 87.3 MB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 32 - Forks: 15
edgardomortiz/Captus
Assembly of Phylogenomic Datasets from High-Throughput Sequencing data
Language: Python - Size: 78.2 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 31 - Forks: 6
LKremer/showTree
showTree can visualize the phylogeny, protein sequences and protein domains of a gene family in one figure.
Language: Python - Size: 65.4 KB - Last synced at: 4 months ago - Pushed at: over 6 years ago - Stars: 30 - Forks: 8
EvolBioInf/phylonium
♥ Fast and Accurate Estimation of Evolutionary Distances
Language: C++ - Size: 881 KB - Last synced at: 3 days ago - Pushed at: 5 months ago - Stars: 29 - Forks: 8
4ment/seqotron
Alignment editor for Mac OS X
Language: Objective-C - Size: 656 KB - Last synced at: 26 days ago - Pushed at: about 8 years ago - Stars: 29 - Forks: 4
datasnakes/OrthoEvolution
An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵
Language: Python - Size: 40.6 MB - Last synced at: 4 days ago - Pushed at: about 2 months ago - Stars: 28 - Forks: 4
crsl4/phylogenetics-class
A course in the theory and practice of phylogenetic inference from DNA sequence data
Language: HTML - Size: 240 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 28 - Forks: 100
JTFouquier/ghost-tree
creating hybrid-gene phylogenetic trees for diversity analyses
Language: Python - Size: 18.5 MB - Last synced at: 10 months ago - Pushed at: about 3 years ago - Stars: 28 - Forks: 20
amnh/PCG
𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search
Language: Haskell - Size: 120 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 28 - Forks: 1
evolbioinfo/booster
Language: C - Size: 642 KB - Last synced at: 5 months ago - Pushed at: over 5 years ago - Stars: 28 - Forks: 2
reslp/phylociraptor
rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference
Language: Python - Size: 3.37 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 27 - Forks: 6
theosanderson/chronumental
Estimating time trees from very large phylogenies
Language: Python - Size: 2.39 MB - Last synced at: 11 days ago - Pushed at: about 1 year ago - Stars: 27 - Forks: 7
C3BI-pasteur-fr/ngphylogeny-django
Language: HTML - Size: 6.86 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 27 - Forks: 22
stajichlab/Phyling
Phyling: phylogenetic inference from annotated genomes
Language: Python - Size: 18.5 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 26 - Forks: 5
hhandika/segul
An ultrafast and memory efficient tool for phylogenomics
Language: Rust - Size: 1.86 MB - Last synced at: 2 days ago - Pushed at: about 1 month ago - Stars: 26 - Forks: 2
JLSteenwyk/orthosnap
a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
Language: Python - Size: 112 MB - Last synced at: 7 days ago - Pushed at: 7 months ago - Stars: 26 - Forks: 1
GDKO/AvP
Automatic evaluation of HGTs
Language: Python - Size: 3.18 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 26 - Forks: 3
hallamlab/TreeSAPP
A Python package for gene-centric taxonomic and functional classification using phylogenetic placement
Language: Python - Size: 133 MB - Last synced at: 15 days ago - Pushed at: about 1 year ago - Stars: 26 - Forks: 4
jbpease/dfoil
DFOIL: Introgression Testing for Five Taxa
Language: Python - Size: 2.64 MB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 26 - Forks: 9
xflouris/libpll
Phylogenetic Likelihood Library
Language: C - Size: 3.06 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 26 - Forks: 7
ropensci/phylotaR
An automated pipeline for retrieving orthologous DNA sequences from GenBank in R
Language: R - Size: 15.2 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 24 - Forks: 9
mpxv-lineages/lineage-designation
Official place for proposals and details around monkeypox virus lineage designations
Language: Python - Size: 930 KB - Last synced at: about 7 hours ago - Pushed at: about 7 hours ago - Stars: 23 - Forks: 3
ms609/TreeTools
Create, modify and analyse phylogenetic trees in R
Language: R - Size: 23 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 23 - Forks: 7
vinuesa/TIB-filoinfo
Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México
Language: Shell - Size: 161 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 23 - Forks: 5
4ment/phylostan
Phylogenetic inference using Stan
Language: Python - Size: 13.3 MB - Last synced at: 8 days ago - Pushed at: 6 months ago - Stars: 23 - Forks: 5
drboothtj/getphylo
a python package for automated generation of phylogenetic trees from genbank files
Language: Python - Size: 75.8 MB - Last synced at: 14 days ago - Pushed at: 6 months ago - Stars: 22 - Forks: 2
FePhyFoFum/PyPHLAWD
Python version of PHLAWD
Language: Python - Size: 12.6 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 21 - Forks: 7
USDA-VS/vSNP
vSNP -- validate SNPs
Language: Python - Size: 68.5 MB - Last synced at: 2 months ago - Pushed at: 12 months ago - Stars: 21 - Forks: 12
jangevaare/PhyloTrees.jl
Phylogenetic trees in Julia
Language: Julia - Size: 295 KB - Last synced at: about 1 month ago - Pushed at: about 4 years ago - Stars: 21 - Forks: 8
molbiodiv/bcgTree
Automatically calculate phylogenetic trees from bacterial core genes
Language: Perl - Size: 19.2 MB - Last synced at: 2 days ago - Pushed at: 4 months ago - Stars: 20 - Forks: 9
Wytamma/beastiary
Real time and remote MCMC trace monitoring with BEASTIARY.
Language: Vue - Size: 54.3 MB - Last synced at: 1 day ago - Pushed at: 4 months ago - Stars: 20 - Forks: 2
computations/root_digger
A tool to root phylogenies
Language: C++ - Size: 8.8 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 20 - Forks: 7
tschuelia/PyPythia
Lightweight python library for predicting the difficulty of alignments in phylogenetics
Language: Python - Size: 8.29 MB - Last synced at: about 11 hours ago - Pushed at: 5 months ago - Stars: 19 - Forks: 1
simonpenel/thirdkind
Drawing reconciled phylogenetic trees allowing 1, 2 or 3 reconcillation levels
Language: Rust - Size: 8.19 MB - Last synced at: 2 days ago - Pushed at: 6 months ago - Stars: 19 - Forks: 0
fmichonneau/phylobase
An R package that provides a base S4 class for comparative methods, incorporating one or more trees and trait data
Language: R - Size: 5.91 MB - Last synced at: about 6 hours ago - Pushed at: over 1 year ago - Stars: 19 - Forks: 0
sishuowang/Solutions_Manual_CME2006_MESA2014
A solutions manual for all excercises in the Ziheng Yang's two seminall books on statistical molecular evolution: Computational Molecular Evolution (Yang 2006) and Molecular Evolution: A Statistical Approach (Yang 2014).
Language: Terra - Size: 89.3 MB - Last synced at: 16 days ago - Pushed at: 17 days ago - Stars: 18 - Forks: 5
gwct/grampa
Gene-tree Reconciliation Algorithm with MUL-trees for Polyploid Analysis
Language: Python - Size: 70.4 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 17 - Forks: 2
4ment/torchtree
A probabilistic framework in PyTorch for phylogenetic models
Language: Jupyter Notebook - Size: 42.6 MB - Last synced at: 26 days ago - Pushed at: 9 months ago - Stars: 17 - Forks: 3
matsengrp/gctree
GCtree: phylogenetic inference of genotype-collapsed trees
Language: Python - Size: 16.2 MB - Last synced at: 20 days ago - Pushed at: about 1 year ago - Stars: 17 - Forks: 2
BioJulia/SubstitutionModels.jl
Biological Sequence Substitution Models for Julia
Language: Julia - Size: 542 KB - Last synced at: 13 days ago - Pushed at: over 2 years ago - Stars: 17 - Forks: 7
rvosa/bio-phylo
Bio::Phylo - Phyloinformatic analysis using Perl
Language: Perl - Size: 77.3 MB - Last synced at: 3 days ago - Pushed at: over 6 years ago - Stars: 17 - Forks: 6
LKremer/MSA_trimmer
Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.
Language: Python - Size: 8.79 KB - Last synced at: 2 months ago - Pushed at: over 6 years ago - Stars: 17 - Forks: 2
ms609/Quartet
R package to calculate the similarity of two trees based on the number of shared four-taxon subtrees (or splits)
Language: C++ - Size: 14.8 MB - Last synced at: 2 days ago - Pushed at: 6 days ago - Stars: 16 - Forks: 5
nextstrain/ncov-clades-schema
Renders SVG schema of SARS-CoV-2 clade as defined by Nextstrain
Language: JavaScript - Size: 383 KB - Last synced at: 19 days ago - Pushed at: 27 days ago - Stars: 16 - Forks: 9
d-j-e/SNPPar
Parallel/Homoplasic SNP Finder
Language: Python - Size: 3.37 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 16 - Forks: 4
moshi4/FastDTLmapper 📦
Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method
Language: Python - Size: 38.9 MB - Last synced at: 11 days ago - Pushed at: over 2 years ago - Stars: 16 - Forks: 4
OnlinePhylo/sts
Sequential Tree Sampler for online phylogenetics
Language: C++ - Size: 10.6 MB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 16 - Forks: 3
arzwa/Whale.jl
Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation
Language: Julia - Size: 4.63 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 15 - Forks: 5
