List of phylogenetics software
Jump to navigation
Jump to search
This content was retrieved from
Wikipedia : http://en.wikipedia.org/wiki/List_of_phylogenetics_softwareThis article needs additional citations for verification. (September 2014) (Learn how and when to remove this template message)

This list of phylogenetics software is a compilation of computational phylogenetics software used to produce phylogenetic trees. Such tools are commonly used in comparative genomics, cladistics, and bioinformatics. Methods for estimating phylogenies include neighborjoining, maximum parsimony (also simply referred to as parsimony), UPGMA, Bayesian phylogenetic inference, maximum likelihood and distance matrix methods.
Name  Description  Methods  Author 

AliGROOVE ^{[1]}  Visualisation of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support  Identification of single taxa which show predominately randomized sequence similarity in comparison with other taxa in a multiple sequence alignment and evaluation of the reliability of node support in a given topology  Patrick Kück, Sandra A Meid, Christian Groß, Bernhard Misof, Johann Wolfgang Wägele. 
ape  RProject package for analysis of phylogenetics and evolution  Provides a large variety of phylogenetics functions  Maintainer: Emmanuel Paradis 
Armadillo Workflow Platform  Workflow platform dedicated to phylogenetic and general bioinformatic analysis  Inference of phylogenetic trees using Distance, Maximum Likelihood, Maximum Parsimony, Bayesian methods and related workflows.  E. Lord, M. Leclercq, A. Boc, A.B. Diallo and V. Makarenkov 
BAliPhy  Simultaneous Bayesian inference of alignment and phylogeny  Bayesian inference, alignment as well as tree search.  M.A. Suchard, B. D. Redelings 
BATWING  Bayesian Analysis of Trees With Internal Node Generation  Bayesian inference, demographic history, population splits  I. J. Wilson, Weale, D.Balding 
BayesPhylogenies  Bayesian inference of trees using Markov chain Monte Carlo methods  Bayesian inference, multiple models, mixture model (autopartitioning)  M. Pagel, A. Meade 
BayesTraits  Analyses trait evolution among groups of species for which a phylogeny or sample of phylogenies is available  Trait analysis  M. Pagel, A. Meade 
BEAST  Bayesian Evolutionary Analysis Sampling Trees  Bayesian inference, relaxed molecular clock, demographic history  A. J. Drummond, A. Rambaut & M. A. Suchard 
BioNumerics  Universal platform for the management, storage and analysis of all types of biological data, including tree and network inference of sequence data.  Neighborjoining, maximum parsimony, UPGMA, maximum likelihood, distance matrix methods,... Calculation of the reliability of trees/branches using bootstrapping, permutation resampling or error resampling.  L. Vauterin & P. Vauterin. 
Bosque  Integrated graphical software to perform phylogenetic analyses, from the importing of sequences to the plotting and graphical edition of trees and alignments  Distance and maximum likelihood methods (through phyml, phylip & treepuzzle)  S. Ramirez, E. Rodriguez. 
BUCKy  Bayesian concordance of gene trees  Bayesian concordance using modified greedy consensus of unrooted quartets  C. Ané, B. Larget, D.A. Baum, S.D. Smith, A. Rokas and B. Larget, S.K. Kotha, C.N. Dewey, C. Ané 
ClustalW  Progressive multiple sequence alignment  Distance matrix/nearest neighbor  Thompson et al. 
Dendroscope ^{[2]}  Tool for visualizing rooted trees and calculating rooted networks  Rooted trees, tanglegrams, consensus networks, hybridization networks  Daniel Huson et al. 
EzEditor ^{[3]}  EzEditor is a javabased sequence alignment editor for rRNA and protein coding genes. It allows manipulation of both DNA and protein sequence alignments for phylogenetic analysis.  Neighbor Joining  Jeon, Y.S. et al. 
fastDNAml  Optimized maximum likelihood (nucleotides only)  Maximum likelihood  G.J. Olsen 
FastTree 2^{[4]}  Fast phylogenetic inference for alignments with up to hundreds of thousands of sequences  Approximate maximum likelihood  M.N. Price, P.S. Dehal, A.P. Arkin 
fitmodel  Fits branchsite codon models without the need of prior knowledge of clades undergoing positive selection  Maximum likelihood  S. Guindon 
Geneious  Geneious provides genome and proteome research tools  Neighborjoining, UPGMA, MrBayes plugin, PHYML plugin, RAxML plugin, FastTree plugin, GARLi plugin, PAUP* Plugin  A. J. Drummond,M.Suchard,V.Lefort et al. 
HyPhy  Hypothesis testing using phylogenies  Maximum likelihood, neighborjoining, clustering techniques, distance matrices  S.L. Kosakovsky Pond, S.D.W. Frost, S.V. Muse 
IQPNNI  Iterative ML treesearch with stopping rule  Maximum likelihood, neighborjoining  L.S. Vinh, A. von Haeseler, B.Q. Minh 
IQTREE^{[5]}  An efficient phylogenomic software by maximum likelihood, as successor of IQPNNI and TREEPUZZLE.  Maximum likelihood, model selection, partitioning scheme finding, AIC, AICc, BIC, ultrafast bootstrapping,^{[6]} branch tests, tree topology tests, likelihood mapping  LamTung Nguyen, O. Chernomor, H.A. Schmidt, A. von Haeseler, B.Q. Minh 
jModelTest 2  A highperformance computing program to carry out statistical selection of bestfit models of nucleotide substitution  Maximum likelihood, AIC, BIC, DT, hLTR, dLTR  D. Darriba, GL. Taboada, R. Doallo, D. Posada 
LisBeth  Threeitem analysis for phylogenetics and biogeography  Threeitem analysis  J. Ducasse, N. Cao & R. ZaragüetaBagils 
MEGA  Molecular Evolutionary Genetics Analysis  Distance, Parsimony and Maximum Composite Likelihood Methods  Tamura K, Dudley J, Nei M & Kumar S 
Mesquite  Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern comparative analyses or population genetics, while others do nonphylogenetic multivariate analysis. It can also be used to build timetrees incorporating a geological timescale, with some optional modules.  Maximum parsimony, distance matrix, maximum likelihood  Wayne Maddison and D. R. Maddison 
MetaPIGA2  Maximum likelihood phylogeny inference multicore program for DNA and protein sequences, and morphological data. Analyses can be performed using an extensive and userfriendly graphical interface or by using batch files. It also implements tree visualization tools, ancestral sequences, and automated selection of best substitution model and parameters.  Maximum likelihood, stochastic heuristics (genetic algorithm, metapopulation genetic algorithm, simulated annealing, etc.), discrete Gamma rate heterogeneity, ancestral state reconstruction, model testing.  Michel C. Milinkovitch and Raphaël Helaers 
Modelgenerator  Model selection (protein or nucleotide)  Maximum likelihood  Thomas Keane 
MOLPHY  Molecular phylogenetics (protein or nucleotide)  Maximum likelihood  J. Adachi and M. Hasegawa 
MrBayes  Posterior probability estimation  Bayesian inference  J. Huelsenbeck, et al. 
Network  Free Phylogenetic Network Software  Median Joining, Reduced Median, Steiner Network  A. Roehl 
Nona  Phylogenetic inference  Maximum parsimony, implied weighting, ratchet  P. Goloboff 
PAML  Phylogenetic analysis by maximum likelihood  Maximum likelihood and Bayesian inference  Z. Yang 
ParaPhylo^{[7]}  Computation of gene and species trees based on eventrelations (orthology, paralogy)  CographEditing and TripleInference  M. Hellmuth, N. Wieseke, M. Lechner, H.P. Lenhof, M. Middendorf, P.F. Stadler 
PartitionFinder  Combined selection of models of molecular evolution and partitioning schemes for DNA and protein alignments.  Maximum likelihood, AIC, AICc, BIC  R. Lanfear, B Calcott, SYW Ho, S Guindon 
PAUP*  Phylogenetic analysis using parsimony (*and other methods)  Maximum parsimony, distance matrix, maximum likelihood  D. Swofford 
phangorn ^{[8]}  Phylogenetic analysis in R  ML, MP, distance matrix, bootstrap, phylogentic networks, bootstrap, model selection, SHtest, SOWHtest  Maintainer: K. Schliep 
Phybase ^{[9]}  an R package for species tree analysis  phylogenetics functions, STAR, NJst, STEAC, maxtree, etc  L. Liu & L. Yu 
phyclust  Phylogenetic Clustering (Phyloclustering)  Maximum likelihood of Finite Mixture Modes  WeiChen Chen 
PHYLIP  Phylogenetic inference package  Maximum parsimony, distance matrix, maximum likelihood  J. Felsenstein 
phyloT  Generates phylogenetic trees in various formats, based on NCBI taxonomy  none  I. Letunic 
PhyloQuart  Quartet implementation (uses sequences or distances)  Quartet method  V. Berry 
PhyML  Fast and accurate estimation of phylogenies using maximum likelihood  Maximum likelihood  S. Guindon & O. Gascuel 
POY  A phylogenetic analysis program that supports multiple kinds of data and can perform alignment and phylogeny inference. A variety of heuristic algorithms have been developed for this purpose.  Maximum parsimony, Maximum likelihood, Chromosome rearrangement, discreet characters, continuous characters, Alignment  A. Varon, N. Lucaroni, L. Hong, W. Wheeler 
ProtTest 3  A highperformance computing program for selecting the model of protein evolution that best fits a given set of aligned sequences  Maximum likelihood, AIC, BIC, DT  D. Darriba, GL. Taboada, R. Doallo, D. Posada 
PyCogent  Software library for genomic biology  Simulating sequences, alignment, controlling third party applications, workflows, querying databases, generating graphics and phylogenetic trees  Knight et al. 
QuickTree  Tree construction optimized for efficiency  Neighborjoining  K. Howe, A. Bateman, R. Durbin 
RAxMLHPC  Randomized Axelerated Maximum Likelihood for High Performance Computing (nucleotides and aminoacids)  Maximum likelihood, simple Maximum parsimony  A. Stamatakis 
SEMPHY  Tree reconstruction using the combined strengths of maximumlikelihood (accuracy) and neighborjoining (speed). SEMPHY has become outdated. The authors now refer users to RAxML, which is superior in both accuracy and speed.  A hybrid maximumlikelihood / neighborjoining method  M. Ninio, E. Privman, T. Pupko, N. Friedman 
sowhat ^{[10]}  Hypothesis testing  SOWH test  Church, Ryan, and Dunn 
SplitsTree ^{[11]}  Tree and network program  Computation, visualization and exploration of phylogenetic trees and networks  D.H. Huson and D. Bryant 
TNT  Phylogenetic inference  Parsimony, weighting, ratchet, tree drift, tree fusing, sectorial searches  P. Goloboff et al. 
TOPALi  Phylogenetic inference  Phylogenetic model selection, Bayesian analysis and Maximum Likelihood phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysis  Iain Milne, Dominik Lindner et al. 
TreeGen  Tree construction given precomputed distance data  Distance matrix  ETH Zurich 
TreeAlign  Efficient hybrid method  Distance matrix and approximate parsimony  J. Hein 
Treefinder  Fast ML tree reconstruction, bootstrap analysis, model selection, hypothesis testing, tree calibration, tree manipulation and visualization, computation of sitewise rates, sequence simulation, many models of evolution (DNA, protein, rRNA, mixed protein, userdefinable), GUI and scripting language  Maximum likelihood, distances, and others  G. Jobb 
TREEPUZZLE  Maximum likelihood and statistical analysis  Maximum likelihood  H.A. Schmidt, K. Strimmer, A. von Haeseler 
TREX (Webserver)  Tree inference and visualization, Horizontal gene transfer detection, multiple sequence alignment  Distance (neighbor joining), Parsimony and Maximum likelihood (PhyML, RAxML) tree inference, MUSCLE, MAFFT and ClustalW sequence alignments and related applications  V. Makarenkov, et al. 
UGENE  Fast and free multiplatform tree editor  based Phylip 3.6 package algorithms  Unipro 
Winclada  GUI and tree editor (requires Nona)  Maximum parsimony, ratchet  K. Nixon 
Xrate  Phylogrammar engine  Rate estimation, branch length estimation, alignment annotation  I. Holmes 
See also
References
 ^ AliGROOVE  visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support; Kueck et al.;BMC Bioinformatics 2014; 15:294
 ^ Huson, DH and C. Scornavacca, Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks. Syst. Biol. 0(0):1–7, 2012. http://sysbio.oxfordjournals.org/content/early/2012/09/24/sysbio.sys062.full.pdf+html
 ^ YoonSeong Jeon, Kihyun Lee, SangCheol Park, BongSoo Kim, YongJoon Cho, SungMin Ha and Jongsik Chun, 10.1099/ijs.0.0593600 IJSEM December 2013 Int J Syst Evol Microbiol 64, 689691
 ^ Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.; Poon, Art F. Y. (10 March 2010). "FastTree 2  Approximately MaximumLikelihood Trees for Large Alignments". PLoS ONE. 5 (3): e9490. doi:10.1371/journal.pone.0009490. PMC 2835736. PMID 20224823.
 ^ Nguyen, LamTung; Chernomor, O; Schmidt, HA; von Haeseler, A; Minh, BQ (Jan 2015). "IQTREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies". Mol Biol Evol. 32 (1): 268–74. doi:10.1093/molbev/msu300. PMC 4271533. PMID 25371430.
 ^ Minh, BQ; Nguyen, MAT; von Haeseler, A (May 2013). "Ultrafast Approximation for Phylogenetic Bootstrap". Mol Biol Evol. 30 (5): 1188–1195. doi:10.1093/molbev/mst024. PMC 3670741. PMID 23418397.
 ^ Phylogenomics with paralogs; Hellmuth et al.; Proc Natl Acad Sci 2015; 112:7
 ^ Schliep, KP (2011). "phangorn: phylogenetic analysis in R". Bioinformatics. 27 (4): 592–593. doi:10.1093/bioinformatics/btq706. PMC 3035803. PMID 21169378.
 ^ Liu L., Yu L. (2010). "an R package for species tree analysis". Bioinformatics. 26 (7): 962–963. doi:10.1093/bioinformatics/btq062. PMID 20156990.
 ^ Church SH, Ryan JF, Dunn CW (2015). "Automation and Evaluation of the SOWH Test with SOWHAT". Syst Biol. 64 (6): 1048–58. doi:10.1093/sysbio/syv055. PMC 4604836. PMID 26231182.CS1 maint: Multiple names: authors list (link)
 ^ Huson, DH; Bryant, D (Feb 2006). "Application of phylogenetic networks in evolutionary studies". Mol Biol Evol. 23 (2): 254–67. doi:10.1093/molbev/msj030. PMID 16221896.
External links
 Complete list of Institut Pasteur phylogeny webservers
 ExPASy List of phylogenetics programs
 A very comprehensive list of phylogenetic tools (reconstruction, visualization, etc.)
 Another list of evolutionary genetics software
 A list of phylogenetic software provided by the Zoological Research Museum A. Koenig
This page is based on the copyrighted Wikipedia article "List of phylogenetics software"; it is used under the Creative Commons
AttributionShareAlike 3.0 Unported License (CCBYSA). You may
redistribute it, verbatim or modified, providing that you comply with
the terms of the CCBYSA