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phylogenetics
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158 search results found
Biopython
⭐
3,918
Official git repository for Biopython (originally converted from CVS)
Ete
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730
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.
Gtdbtk
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383
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Raxml Ng
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339
RAxML Next Generation: faster, easier-to-use and more flexible
Beast2
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228
Bayesian Evolutionary Analysis by Sampling Trees
Vcf2phylip
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216
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
Mrbayes
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201
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:
Treetime
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196
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
Phangorn
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196
Phylogenetic analysis in R
Hyphy
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190
HyPhy: Hypothesis testing using Phylogenies
Beast Mcmc
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166
Bayesian Evolutionary Analysis Sampling Trees
Phyml
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156
PhyML -- Phylogenetic estimation using (Maximum) Likelihood
Tskit
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131
Population-scale genomics
Iq Tree
⭐
125
Efficient phylogenomic software by maximum likelihood
Usher
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112
Ultrafast Sample Placement on Existing Trees
Buddysuite
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105
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
Phyx
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100
phylogenetics tools for linux (and other mostly posix compliant) computers
Cafe5
⭐
100
Version 5 of the CAFE phylogenetics software
Taxonium
⭐
90
A tool for exploring very large trees in the browser
Cogent3
⭐
79
Comparative Genomics Toolkit 3
Baltic
⭐
74
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).
Cafe
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71
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
Epa Ng
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66
Massively parallel phylogenetic placement of genetic sequences
Trifusion
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61
Streamlining phylogenomic data gathering, processing and visualization
Genesis
⭐
54
A library for working with phylogenetic and population genetic data.
Microbetrace
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53
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
R2g
⭐
49
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
Gappa
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49
A toolkit for analyzing and visualizing phylogenetic (placement) data
Clipkit
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44
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
Phykit
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44
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
Babette
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40
babette is an R package to work with BEAST2
Phylopandas
⭐
39
Pandas DataFrames for phylogenetics
Get_phylomarkers
⭐
39
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
Aniclustermap
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38
A tool for drawing ANI clustermap between all-vs-all microbial genomes
Mpox
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37
Nextstrain build for mpox virus
Archaeopteryx Js
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37
Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.
Icytree
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37
Browser-based utility for phylogenetic tree visualisation.
Favites
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35
FAVITES (FrAmework for VIral Transmission and Evolution Simulation)
Itolapi
⭐
31
Python API for the Interactive Tree of Life (iTOL)
Phylo.jl
⭐
29
Simple phylogenetic trees in Julia to work with Diversity.jl - https://github.com/EcoJulia/Diversity.jl
Orthoevolution
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28
An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵
Pcg
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28
𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search
Busco_phylogenomics
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26
BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins
Jstreeview
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25
Interactive phylogenetic tree viewer/editor
Phylotar
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24
An automated pipeline for retrieving orthologous DNA sequences from GenBank in R
Q2 Qemistree
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24
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
Phylociraptor
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23
rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference
Phylogenetics Class
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23
A course in the theory and practice of phylogenetic inference from DNA sequence data
Ghost Tree
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23
creating hybrid-gene phylogenetic trees for diversity analyses
Treesapp
⭐
22
A Python package for gene-centric taxonomic and functional classification using phylogenetic placement
Ngphylogeny Django
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22
Seqotron
⭐
21
Alignment editor for Mac OS X
Phylostan
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21
Phylogenetic inference using Stan
Ufcg
⭐
20
UFCG: Universal Fungal Core Genes
Root_digger
⭐
19
A tool to root phylogenies
Phylonium
⭐
19
♥ Fast and Accurate Estimation of Evolutionary Distances
Pastml
⭐
19
Ancestral character reconstruction and visualisation for rooted phylogenetic trees
Chronumental
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18
Estimating time trees from very large phylogenies
Bcgtree
⭐
18
Automatically calculate phylogenetic trees from bacterial core genes
Orthosnap
⭐
16
a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
Phylobase
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16
An R package that provides a base S4 class for comparative methods, incorporating one or more trees and trait data
Substitutionmodels.jl
⭐
16
Biological Sequence Substitution Models for Julia
Pyphlawd
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16
Python version of PHLAWD
Lineage Designation
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16
Official place for proposals and details around monkeypox virus lineage designations
Snppar
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15
Parallel/Homoplasic SNP Finder
Libpll
⭐
15
Phylogenetic Likelihood Library
Topiary
⭐
15
Python framework for doing ancestral sequence reconstruction
Bio Phylo
⭐
15
Bio::Phylo - Phyloinformatic analysis using Perl
Sts
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15
Sequential Tree Sampler for online phylogenetics
Treetools
⭐
15
Create, modify and analyse phylogenetic trees in R
Dfoil
⭐
15
DFOIL: Introgression Testing for Five Taxa
Physher
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14
Phylogenetic analysis of genetic data
Beastiary
⭐
14
Real time and remote MCMC trace monitoring with BEASTIARY.
Plantphylomoji
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14
Dataset and scripts to create a Phylogeny of Plant Emojis
Booster
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14
Tib Filoinfo
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14
Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México
Cafeplotter
⭐
13
A tool for plotting CAFE5 gene family expansion/contraction result
Rnexml
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13
Implementing semantically rich NeXML I/O in R
Vsnp
⭐
13
vSNP -- validate SNPs
Beautier
⭐
13
R package to generate the same BEAST2 XML parameter files as generated by BEAUti 2
Splitstree6
⭐
13
SplitsTree Community Edition
Wqfm 2020
⭐
13
wQFM implementation in Java
Phylotrees.jl
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13
Phylogenetic trees in Julia
Phylotoast
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12
Tools for phylogenetic data analysis including visualization and cluster-computing support.
Avp
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12
Automatic evaluation of HGTs
Gctree
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12
GCtree: phylogenetic inference of genotype-collapsed trees
Strainhub
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12
Welcome to the StrainHub Repo - Files and Data - StrainHub Online:
Multree
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12
Performs MCMCglmm on multiple phylogenetic trees
Exelixis
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12
Interactive and easy-to-use phylogenetic tree viewer for the web
Scripts
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11
Random scripts, mostly for dealing with RADseq data and DNA sequence alignments
Phydms
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11
phylogenetic analyses informed by deep mutational scanning data
Baltic
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11
baltic - adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. This fork will no longer receive updates, so any further development to baltic is going to happen at https://github.com/evogytis/baltic.
Phylogenetics
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11
Algorithms and datastructures for phylogenetics
Segul
⭐
11
An ultrafast and memory efficient tool for phylogenomics
Raxml_ascbias
⭐
11
Script for removing or counting invariant sites for the RAxML ascertainment bias corrections
Pypythia
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11
Lightweight python library for predicting the difficulty of alignments in phylogenetics
Python Nexus
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11
python-nexus - Generic nexus (.nex, .trees) reader/writer for python
Datelife
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11
R package containing datelife's core functionality
Phylopath
⭐
10
Perform phylogenetic path analysis in R.
Phylosamp
⭐
10
The R package 'phylosamp' implements novel tools that estimate the probability of transmission between two cases given phylogenetic linkage and sample size calculations for phylogenetic studies.
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