phylogenetics | Topic | Ecosyste.ms: Repos

Topic: "phylogenetics"

biopython/biopython

Official git repository for Biopython (originally converted from CVS)

Language: Python - Size: 71.5 MB - Last synced at: 5 days ago - Pushed at: about 2 months ago - Stars: 4,597 - Forks: 1,791

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: 5 days ago - Pushed at: 5 days ago - Stars: 827 - Forks: 219

Ecogenomics/GTDBTk

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

Language: Python - Size: 28.8 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 517 - Forks: 84

amkozlov/raxml-ng

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

Language: C++ - Size: 1.36 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 424 - Forks: 63

CompEvol/beast2

Bayesian Evolutionary Analysis by Sampling Trees

Language: Java - Size: 93.6 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 248 - Forks: 84

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: about 1 month ago - Stars: 243 - Forks: 84

neherlab/treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

Language: Jupyter Notebook - Size: 17.9 MB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 242 - Forks: 57

veg/hyphy

HyPhy: Hypothesis testing using Phylogenies

Language: HyPhy - Size: 57.3 MB - Last synced at: 3 days ago - Pushed at: 10 days ago - Stars: 232 - Forks: 70

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: over 1 year ago - Pushed at: almost 2 years ago - Stars: 232 - Forks: 80

KlausVigo/phangorn

Phylogenetic analysis in R

Language: R - Size: 132 MB - Last synced at: 4 days ago - Pushed at: 20 days ago - Stars: 207 - Forks: 40

beast-dev/beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees

Language: Java - Size: 200 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 204 - Forks: 76

stephaneguindon/phyml

PhyML -- Phylogenetic estimation using (Maximum) Likelihood

Language: C - Size: 71.4 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 183 - Forks: 63

Cibiv/IQ-TREE 📦

Efficient phylogenomic software by maximum likelihood

Language: C++ - Size: 65.4 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 180 - Forks: 45

tskit-dev/tskit

Population-scale Ancestral Recombination Graph (ARG) library

Language: Python - Size: 19.4 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 162 - Forks: 77

hahnlab/CAFE5

Version 5 of the CAFE phylogenetics software

Language: C++ - Size: 3.13 MB - Last synced at: 2 days ago - Pushed at: 3 months ago - Stars: 133 - Forks: 25

cogent3/cogent3

Comparative Genomics Toolkit 3

Language: Python - Size: 45 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 130 - Forks: 65

yatisht/usher

Ultrafast Sample Placement on Existing Trees

Language: C++ - Size: 41.4 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 127 - Forks: 42

biologyguy/BuddySuite

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

Language: Python - Size: 269 MB - Last synced at: 16 days ago - Pushed at: over 3 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: 4 months ago - Pushed at: 4 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: 2 days ago - Pushed at: about 4 years ago - Stars: 116 - Forks: 37

theosanderson/taxonium

A tool for exploring large trees in the browser

Language: TypeScript - Size: 258 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 109 - Forks: 23

husonlab/splitstree6

SplitsTree App

Language: Java - Size: 239 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 109 - Forks: 8

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: 34.7 MB - Last synced at: 17 days ago - Pushed at: about 1 month ago - Stars: 101 - Forks: 31

CDCgov/MicrobeTrace Fork of AABoyles/MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

Language: TypeScript - Size: 136 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 92 - Forks: 42

ODiogoSilva/TriFusion

Streamlining phylogenomic data gathering, processing and visualization

Language: Python - Size: 100 MB - Last synced at: 29 days ago - Pushed at: over 6 years ago - Stars: 88 - Forks: 23

pierrebarbera/epa-ng

Massively parallel phylogenetic placement of genetic sequences

Language: C++ - Size: 32.5 MB - Last synced at: about 1 month ago - Pushed at: almost 3 years ago - Stars: 82 - Forks: 8

moshi4/ANIclustermap

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

Language: Python - Size: 184 MB - Last synced at: about 11 hours ago - Pushed at: 23 days ago - Stars: 80 - Forks: 10

JLSteenwyk/ClipKIT

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

Language: Python - Size: 25.8 MB - Last synced at: 1 day ago - Pushed at: 3 months ago - Stars: 73 - Forks: 5

Zsailer/phylopandas

Pandas DataFrames for phylogenetics

Language: Python - Size: 982 KB - Last synced at: 5 days ago - Pushed at: almost 4 years ago - Stars: 73 - 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: 23 days ago - Pushed at: 23 days ago - Stars: 69 - Forks: 8

jamiemcg/BUSCO_phylogenomics

BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins

Language: Python - Size: 347 KB - Last synced at: about 2 months ago - Pushed at: 8 months ago - Stars: 64 - Forks: 9

lczech/genesis

A library for working with phylogenetic and population genetic data.

Language: C++ - Size: 14.6 MB - Last synced at: 6 days ago - Pushed at: about 1 month ago - Stars: 61 - Forks: 12

lczech/gappa

A toolkit for analyzing and visualizing phylogenetic placement data

Language: C++ - Size: 11.3 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 60 - 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: 2 days ago - Pushed at: 4 months ago - Stars: 55 - Forks: 9

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: 10 months ago - Pushed at: about 4 years ago - Stars: 48 - Forks: 2

nextstrain/mpox

Nextstrain build for mpox virus

Language: Python - Size: 33.3 MB - Last synced at: 6 days ago - Pushed at: 24 days ago - Stars: 46 - Forks: 21

lh3/jstreeview

Interactive phylogenetic tree viewer/editor

Language: JavaScript - Size: 31.3 KB - Last synced at: 19 days ago - Pushed at: almost 2 years ago - Stars: 46 - Forks: 3

ropensci/babette

babette is an R package to work with BEAST2

Language: R - Size: 10.2 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 45 - Forks: 6

cmzmasek/archaeopteryx-js

Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.

Language: JavaScript - Size: 7.22 MB - Last synced at: 28 days ago - Pushed at: 11 months ago - Stars: 41 - Forks: 14

albertyw/itolapi

Python API for the Interactive Tree of Life (iTOL)

Language: Python - Size: 679 KB - Last synced at: about 3 hours ago - Pushed at: about 1 month ago - Stars: 38 - Forks: 11

harmslab/topiary

Python framework for doing ancestral sequence reconstruction

Language: Python - Size: 60.9 MB - Last synced at: about 1 month ago - Pushed at: 11 months ago - Stars: 38 - Forks: 6

niemasd/FAVITES

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)

Language: Python - Size: 25.3 MB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 38 - Forks: 4

tgvaughan/icytree

Browser-based utility for phylogenetic tree visualisation.

Language: JavaScript - Size: 2.92 MB - Last synced at: over 1 year ago - Pushed at: almost 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: 153 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 36 - Forks: 16

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 2 months ago - Pushed at: over 2 years ago - Stars: 36 - Forks: 5

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: 12 days ago - Pushed at: 6 months ago - Stars: 35 - Forks: 13

TurakhiaLab/ROADIES

Tool for fully-automated inference of species trees from raw genome assemblies

Language: Python - Size: 279 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 33 - Forks: 3

evolbioinfo/pastml

Ancestral character reconstruction and visualisation for rooted phylogenetic trees

Language: Python - Size: 35.9 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 32 - Forks: 6

steineggerlab/ufcg

UFCG: Universal Fungal Core Genes

Language: Java - Size: 71.1 MB - Last synced at: about 1 month ago - Pushed at: 4 months ago - Stars: 32 - Forks: 0

biocore/q2-qemistree

Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".

Language: Python - Size: 87.3 MB - Last synced at: 12 days ago - Pushed at: about 2 years ago - Stars: 32 - Forks: 15

JLSteenwyk/orthofisher

a broadly applicable tool for automated gene identification and retrieval

Language: Python - Size: 81.9 MB - Last synced at: about 12 hours ago - Pushed at: 6 months ago - Stars: 31 - Forks: 1

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: 17 days ago - Pushed at: about 6 years ago - Stars: 30 - Forks: 8

moshi4/CafePlotter

A tool for plotting CAFE5 gene family expansion/contraction result

Language: Python - Size: 3.77 MB - Last synced at: 8 days ago - Pushed at: over 1 year ago - Stars: 29 - Forks: 3

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: about 1 month ago - Pushed at: about 1 month ago - Stars: 28 - Forks: 100

datasnakes/OrthoEvolution

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

Language: Python - Size: 40.7 MB - Last synced at: 10 days ago - Pushed at: 6 months ago - Stars: 28 - Forks: 4

JTFouquier/ghost-tree

creating hybrid-gene phylogenetic trees for diversity analyses

Language: Python - Size: 18.5 MB - Last synced at: 7 months ago - Pushed at: almost 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: about 1 year ago - Pushed at: almost 3 years ago - Stars: 28 - Forks: 1

evolbioinfo/booster

Language: C - Size: 642 KB - Last synced at: about 1 month ago - Pushed at: about 5 years ago - Stars: 28 - Forks: 2

4ment/seqotron

Alignment editor for Mac OS X

Language: Objective-C - Size: 656 KB - Last synced at: about 1 month ago - Pushed at: almost 8 years ago - Stars: 28 - Forks: 4

EvolBioInf/phylonium

♥ Fast and Accurate Estimation of Evolutionary Distances

Language: C++ - Size: 855 KB - Last synced at: about 1 month 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: about 1 year ago - Pushed at: about 2 years ago - Stars: 27 - Forks: 22

hhandika/segul

An ultrafast and memory efficient tool for phylogenomics

Language: Rust - Size: 1.85 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 26 - Forks: 2

GDKO/AvP

Automatic evaluation of HGTs

Language: Python - Size: 3.18 MB - Last synced at: 4 months ago - Pushed at: 4 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: 7 days ago - Pushed at: 9 months ago - Stars: 26 - Forks: 4

theosanderson/chronumental

Estimating time trees from very large phylogenies

Language: Python - Size: 2.39 MB - Last synced at: 2 days ago - Pushed at: 10 months ago - Stars: 26 - Forks: 7

jbpease/dfoil

DFOIL: Introgression Testing for Five Taxa

Language: Python - Size: 2.64 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 26 - Forks: 9

xflouris/libpll

Phylogenetic Likelihood Library

Language: C - Size: 3.06 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 26 - Forks: 7

edgardomortiz/Captus

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

Language: Python - Size: 77.9 MB - Last synced at: about 17 hours ago - Pushed at: about 18 hours ago - Stars: 25 - Forks: 6

reslp/phylociraptor

rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference

Language: Python - Size: 3.36 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 25 - Forks: 6

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: about 1 month ago - Pushed at: 3 months ago - Stars: 25 - Forks: 1

4ment/phylostan

Phylogenetic inference using Stan

Language: Python - Size: 13.3 MB - Last synced at: 14 days ago - Pushed at: 3 months ago - Stars: 24 - Forks: 5

ms609/TreeTools

Create, modify and analyse phylogenetic trees in R

Language: R - Size: 18.5 MB - Last synced at: 17 days ago - Pushed at: 20 days ago - Stars: 23 - Forks: 7

mpxv-lineages/lineage-designation

Official place for proposals and details around monkeypox virus lineage designations

Language: Python - Size: 858 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 23 - Forks: 3

ropensci/phylotaR

An automated pipeline for retrieving orthologous DNA sequences from GenBank in R

Language: R - Size: 15.3 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 23 - Forks: 8

vinuesa/TIB-filoinfo

Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México

Language: Shell - Size: 160 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 22 - 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: 7 days ago - Pushed at: 3 months ago - Stars: 22 - Forks: 1

FePhyFoFum/PyPHLAWD

Python version of PHLAWD

Language: Python - Size: 12.6 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 21 - Forks: 7

jangevaare/PhyloTrees.jl

Phylogenetic trees in Julia

Language: Julia - Size: 295 KB - Last synced at: about 1 month ago - Pushed at: over 3 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: 12 days ago - Pushed at: 13 days 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: 9 days ago - Pushed at: 16 days ago - Stars: 20 - Forks: 2

USDA-VS/vSNP

vSNP -- validate SNPs

Language: Python - Size: 68.5 MB - Last synced at: about 1 month ago - Pushed at: 8 months ago - Stars: 20 - Forks: 12

computations/root_digger

A tool to root phylogenies

Language: C++ - Size: 8.8 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 20 - Forks: 7

simonpenel/thirdkind

Drawing reconciled phylogenetic trees allowing 1, 2 or 3 reconcillation levels

Language: Rust - Size: 8.19 MB - Last synced at: 23 days ago - Pushed at: 3 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: 10 days ago - Pushed at: over 1 year ago - Stars: 19 - Forks: 0

matsengrp/gctree

GCtree: phylogenetic inference of genotype-collapsed trees

Language: Python - Size: 16.2 MB - Last synced at: 20 days ago - Pushed at: 9 months ago - Stars: 18 - Forks: 2

tschuelia/PyPythia

Lightweight python library for predicting the difficulty of alignments in phylogenetics

Language: Python - Size: 8.29 MB - Last synced at: 24 days ago - Pushed at: about 2 months ago - Stars: 17 - Forks: 0

BioJulia/SubstitutionModels.jl

Biological Sequence Substitution Models for Julia

Language: Julia - Size: 542 KB - Last synced at: about 7 hours ago - Pushed at: about 2 years ago - Stars: 17 - Forks: 7

LKremer/MSA_trimmer

Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.

Language: Python - Size: 8.79 KB - Last synced at: 17 days ago - Pushed at: about 6 years ago - Stars: 17 - Forks: 2

gwct/grampa

Gene-tree Reconciliation Algorithm with MUL-trees for Polyploid Analysis

Language: Python - Size: 70.4 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 16 - Forks: 2

4ment/torchtree

A probabilistic framework in PyTorch for phylogenetic models

Language: Jupyter Notebook - Size: 42.6 MB - Last synced at: 9 days ago - Pushed at: 6 months ago - Stars: 16 - Forks: 3

d-j-e/SNPPar

Parallel/Homoplasic SNP Finder

Language: Python - Size: 3.37 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 16 - Forks: 4

rvosa/bio-phylo

Bio::Phylo - Phyloinformatic analysis using Perl

Language: Perl - Size: 77.3 MB - Last synced at: about 2 months ago - Pushed at: almost 6 years ago - Stars: 16 - Forks: 6

OnlinePhylo/sts

Sequential Tree Sampler for online phylogenetics

Language: C++ - Size: 10.6 MB - Last synced at: over 1 year ago - Pushed at: about 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: 27 days ago - Pushed at: 27 days ago - Stars: 15 - Forks: 5

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: 14 days ago - Pushed at: about 1 month ago - Stars: 15 - Forks: 5

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: 8 days ago - Pushed at: over 2 years ago - Stars: 15 - Forks: 4