List of phylogenetics software

Last updated

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 neighbor-joining, maximum parsimony (also simply referred to as parsimony), unweighted pair group method with arithmetic mean (UPGMA), Bayesian phylogenetic inference, maximum likelihood, and distance matrix methods.

Contents

List

NameDescriptionMethodsAuthor
ADMIXTOOLS [1] R software package that contains the qpGraph, qpAdm, qpWave, and qpDstat programs Nick Patterson, David Reich
AncesTree [2] An algorithm for clonal tree reconstruction from multi-sample cancer sequencing data.Maximum Likelihood, Integer Linear Programming (ILP)M. El-Kebir, L. Oesper, H. Acheson-Field, B. J. Raphael
AliGROOVE [3] Visualisation of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch supportIdentification 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 topologyPatrick Kück, Sandra A Meid, Christian Groß, Bernhard Misof, Johann Wolfgang Wägele.
ape [4] R-Project package for analysis of phylogenetics and evolutionProvides a large variety of phylogenetics functionsMaintainer: Emmanuel Paradis
Armadillo Workflow Platform [5] Workflow platform dedicated to phylogenetic and general bioinformatic analysisInference of phylogenetic trees using Distance, Maximum Likelihood, Maximum Parsimony, Bayesian methods and related workflowsE. Lord, M. Leclercq, A. Boc, A.B. Diallo and V. Makarenkov
BAli-Phy [6] Simultaneous Bayesian inference of alignment and phylogenyBayesian inference, alignment as well as tree searchM.A. Suchard, B. D. Redelings
BATWING [7] Bayesian Analysis of Trees With Internal Node GenerationBayesian inference, demographic history, population splitsI. J. Wilson, Weale, D.Balding
BayesPhylogenies [8] Bayesian inference of trees using Markov chain Monte Carlo methodsBayesian inference, multiple models, mixture model (auto-partitioning)M. Pagel, A. Meade
BayesTraits [9] Analyses trait evolution among groups of species for which a phylogeny or sample of phylogenies is availableTrait analysisM. Pagel, A. Meade
BEAST [10] Bayesian Evolutionary Analysis Sampling TreesBayesian inference, relaxed molecular clock, demographic historyA. J. Drummond, M. A. Suchard, D Xie & A. Rambaut
BioNumerics Universal platform for the management, storage and analysis of all types of biological data, including tree and network inference of sequence dataNeighbor-joining, maximum parsimony, UPGMA, maximum likelihood, distance matrix methods,... Calculation of the reliability of trees/branches using bootstrapping, permutation resampling or error resamplingL. Vauterin & P. Vauterin.
BosqueIntegrated graphical software to perform phylogenetic analyses, from the importing of sequences to the plotting and graphical edition of trees and alignmentsDistance and maximum likelihood methods (through PhyML, PHYLIP, Tree-Puzzle)S. Ramirez, E. Rodriguez.
BUCKy [11] Bayesian concordance of gene treesBayesian 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
Canopy [12] Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencingMaximum Likelihood, Markov Chain Monte Carlo (MCMC) methodsY. Jiang, Y. Qiu, A. J. Minn, and N. R. Zhang
CGRphylo [13] CGR method for accurate classification and tracking of rapidly evolving virusesChaos Game Representation (CGR) method, based on concepts of statistical physicsAmarinder Singh Thind, Somdatta Sinha
CITUPClonality Inference in Tumors Using PhylogenyExhaustive search, Quadratic Integer Programming (QIP)S. Malikic, A.W. McPherson, N. Donmez, C.S. Sahinalp
ClustalWProgressive multiple sequence alignmentDistance matrix/nearest neighborThompson et al. [14]
CoalEvolSimulation of DNA and protein evolution along phylogenetic trees (that can also be simulated with the coalescent)Simulation of multiple sequence alignments of DNA or protein sequencesM. Arenas, D. Posada
CodABCCoestimation of substitution, recombination and dN/dS in protein sequencesApproximate Bayesian computationM. Arenas, J.S. Lopes, M.A. Beaumont, D. Posada
Dendroscope [15] Tool for visualizing rooted trees and calculating rooted networksRooted trees, tanglegrams, consensus networks, hybridization networksDaniel Huson et al.
EXACT [16] [17] EXACT is based on the perfect phylogeny model, and uses a very fast homotopy algorithm to evaluate the fitness of different trees, and then it brute forces the tree search using GPUs, or multiple CPUs, on the same or on different machinesBrute force search and homotopy algorithmJia B., Ray S., Safavi S., Bento J.
EzEditor [18] EzEditor is a java-based sequence alignment editor for rRNA and protein coding genes. It allows manipulation of both DNA and protein sequence alignments for phylogenetic analysisMultiple sequence alignment and editingY.-S. Jeon, K. Lee, S.-C. Park, B.-S. Kim, Y.-J. Cho, S.-M. Ha, and J. Chun
fastDNAmlOptimized maximum likelihood (nucleotides only)Maximum likelihoodG.J. Olsen
FastTree 2 [19] Fast phylogenetic inference for alignments with up to hundreds of thousands of sequencesApproximate maximum likelihoodM.N. Price, P.S. Dehal, A.P. Arkin
fitmodelFits branch-site codon models without the need of prior knowledge of clades undergoing positive selectionMaximum likelihoodS. Guindon
Geneious Geneious provides genome and proteome research toolsNeighbor-joining, UPGMA, MrBayes plugin, PhyML plugin, RAxML plugin, FastTree plugin, GARLi plugin, PAUP* PluginA. J. Drummond, M.Suchard, V.Lefort et al.
HyPhy Hypothesis testing using phylogeniesMaximum likelihood, neighbor-joining, clustering techniques, distance matricesS.L. Kosakovsky Pond, S.D.W. Frost, S.V. Muse
INDELible [20] Simulation of DNA/protein sequence evolutionSimulationW. Fletcher, Z. Yang
IQPNNI (No longer maintained; superseded by IQ-TREE) [21] Iterative ML treesearch with stopping ruleMaximum likelihood, neighbor-joiningL.S. Vinh, A. von Haeseler, B.Q. Minh
IQ-Tree [22] [23] An efficient phylogenomic software by maximum likelihood, as successor of IQPNNI and Tree-PuzzleMaximum likelihood, model selection, partitioning scheme finding, AIC, AICc, BIC, ultrafast bootstrapping, [24] branch tests, tree topology tests, likelihood mappingLam-Tung Nguyen, O. Chernomor, H.A. Schmidt, A. von Haeseler, B.Q. Minh
jModelTest 2A high-performance computing program to carry out statistical selection of best-fit models of nucleotide substitutionMaximum likelihood, AIC, BIC, DT, hLTR, dLTRD. Darriba, GL. Taboada, R. Doallo, D. Posada
JolyTree [25] [26] An alignment-free bioinformatics procedure to infer distance-based phylogenetic trees from genome assemblies, specifically designed to quickly infer trees from genomes belonging to the same genus MinHash-based pairwise genome distance, Balanced Minimum Evolution (BME), ratchet-based BME tree search, Rate of Elementary QuartetsA. Criscuolo
LisBethThree-item analysis for phylogenetics and biogeographyThree-item analysisJ. Ducasse, N. Cao & R. Zaragüeta-Bagils
MEGA Molecular Evolutionary Genetics AnalysisDistance, Parsimony and Maximum Composite Likelihood MethodsTamura K, Dudley J, Nei M & Kumar S
MegAlign ProMegAlign Pro is part of DNASTAR's Lasergene Molecular Biology package. This application performs multiple and pairwise sequence alignments, provides alignment editing, and generates phylogenetic trees.Maximum Likelihood (RAxML) and Neighbor-Joining DNASTAR
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 non-phylogenetic 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
MetaPIGA2Maximum likelihood phylogeny inference multi-core program for DNA and protein sequences, and morphological data. Analyses can be performed using an extensive and user-friendly 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 testingMichel C. Milinkovitch and Raphaël Helaers
MicrobeTrace MicrobeTrace is a free, browser-based web application.2D and 3D network visualization tool, Neighbor-joining tree visualization, Gantt charts, bubbles charts, networks visualized on maps, flow diagrams, aggregate tables, epi curves, histograms, alignment viewer, and much more.Ellsworth M. Campbell, Anthony Boyles, Anupama Shankar, Jay Kim, Sergey Knyazev, Roxana Cintron, William M. Switzer [27]
MNHN-Tree-Tools MNHN-Tree-Tools is an opensource phylogenetics inference software working on nucleic and protein sequences.Clustering of DNA or protein sequences and phylogenetic tree inference from a set of sequences. At the core it employs a distance-density based approach.Thomas Haschka, Loïc Ponger, Christophe Escudé and Julien Mozziconacci [28]
ModelgeneratorModel selection (protein or nucleotide)Maximum likelihoodThomas Keane
MOLPHYMolecular phylogenetics (protein or nucleotide)Maximum likelihoodJ. Adachi and M. Hasegawa
MorphoBank Web application to organize trait data (morphological characters) for tree buildingfor use with Maximum Parsimony (via the CIPRES portal), Maximum Likelihood, and Bayesian analysis)O'Leary, M. A., and S. Kaufman, [29] also K. Alphonse
MrBayes Posterior probability estimation Bayesian inference J. Huelsenbeck, et al. [30]
NetworkFree Phylogenetic Network SoftwareMedian Joining, Reduced Median, Steiner NetworkA. Roehl
NonaPhylogenetic inferenceMaximum parsimony, implied weighting, ratchetP. Goloboff
PAML [31] Phylogenetic analysis by maximum likelihoodMaximum likelihood and Bayesian inference Z. Yang
ParaPhylo [32] Computation of gene and species trees based on event-relations (orthology, paralogy)Cograph-Editing and Triple-InferenceHellmuth
PartitionFinder [33] Combined selection of models of molecular evolution and partitioning schemes for DNA and protein alignmentsMaximum likelihood, AIC, AICc, BICR. Lanfear, B Calcott, SYW Ho, S Guindon
PASTISR package for phylogenetic assemblyR, two‐stage Bayesian inference using MrBayes 3.2Thomas et al. 2013 [34]
PAUP* Phylogenetic analysis using parsimony (*and other methods)Maximum parsimony, distance matrix, maximum likelihoodD. Swofford
phangorn [35] Phylogenetic analysis in RML, MP, distance matrix, bootstrap, phylogentic networks, bootstrap, model selection, SH-test, SOWH-testMaintainer: K. Schliep
Phybase [36] an R package for species tree analysisphylogenetics functions, STAR, NJst, STEAC, maxtree, etcL. Liu & L. Yu
phyclustPhylogenetic Clustering (Phyloclustering)Maximum likelihood of Finite Mixture ModesWei-Chen Chen
PHYLIP PHYLogeny Inference PackageMaximum parsimony, distance matrix, maximum likelihood J. Felsenstein
phyloTGenerates phylogenetic trees in various formats, based on NCBI taxonomynoneI. Letunic
PhyloQuartQuartet implementation (uses sequences or distances)Quartet methodV. Berry
PhyloWGSReconstructing subclonal composition and evolution from whole-genome sequencing of tumorsMCMCA. G. Deshwar, S. Vembu, C. K. Yung, G. H. Jang, L. Stein, and Q. Morris
PhyML [37] Fast and accurate estimation of phylogenies using maximum likelihoodMaximum likelihoodS. Guindon & O. Gascuel
phyx [38] Unix/Linux command line phylogenetic toolsExplore, manipulate, analyze, and simulate phylogenetic objects (alignments, trees, and MCMC logs)J.W. Brown, J.F. Walker, and S.A. Smith
POYA 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 purposeMaximum parsimony, Maximum likelihood, Chromosome rearrangement, discreet characters, continuous characters, AlignmentA. Varon, N. Lucaroni, L. Hong, W. Wheeler
ProtASR2 [39] Ancestral reconstruction of protein sequences accounting for folding stabilityMaximum likelihood, substitution modelsM. Arenas, U. Bastolla
ProtEvolSimulation of protein sequences under structurally constrained substitution modelsSimulating sequences, substitution modelsM. Arenas, A. Sanchez-Cobos, U. Bastolla U
ProteinEvolverSimulation of protein sequences along phylogenies under empirical and structurally constrained substitution models of protein evolutionSimulating sequences forward in time, substitution modelsM. Arenas, H.G. Dos Santos, D. Posada, U. Bastolla
ProteinEvolverABC [40] Coestimation of recombination and substitution rates in protein sequencesApproximate Bayesian computationM. Arenas
ProteinModelerABC [41] Selection among site-dependent structurally constrained substitution models of protein evolutionApproximate Bayesian computationD. Ferreiro et al
ProtTest3A high-performance computing program for selecting the model of protein evolution that best fits a given set of aligned sequencesMaximum likelihood, AIC, BIC, DTD. Darriba, GL. Taboada, R. Doallo, D. Posada
PyCogentSoftware library for genomic biologySimulating sequences, alignment, controlling third party applications, workflows, querying databases, generating graphics and phylogenetic treesKnight et al.
QuickTreeTree construction optimized for efficiencyNeighbor-joiningK. Howe, A. Bateman, R. Durbin
RAxML-HPCRandomized Axelerated Maximum Likelihood for High Performance Computing (nucleotides and aminoacids)Maximum likelihood, simple Maximum parsimonyA. Stamatakis
RAxML-NG [42] Randomized Axelerated Maximum Likelihood for High Performance Computing (nucleotides and aminoacids) Next GenerationMaximum likelihood, simple Maximum parsimonyA. Kozlov, D. Darriba, T. Flouri, B. Morel, A. Stamatakis
SEMPHYTree reconstruction using the combined strengths of maximum-likelihood (accuracy) and neighbor-joining (speed). SEMPHY has become outdated. The authors now refer users to RAxML, which is superior in accuracy and speed.A hybrid maximum-likelihood – neighbor-joining methodM. Ninio, E. Privman, T. Pupko, N. Friedman
SGWESimulation of genome-wide evolution along phylogenetic treesSimulating genome-wide sequences forward timeArenas M., Posada D.
SimPlot++ [43] Sequence similarity plots (SimPlots [44] ), detection of intragenic and intergenic recombination events, bootscan analysis [45] and sequence similarity networksSimPlot using different nucleotide/protein distance models; Phi, χ2 and NSS recombination tests; Sequence similarity network analysisS. Samson, E. Lord, V. Makarenkov
sowhat [46] Hypothesis testingSOWH testSamuel H Church, Joseph F Ryan, and Casey W Dunn
Splatche3 [47] Simulation of genetic data under diverse spatially explicit evolutionary scenariosCoalescent, molecular evolution, DNA sequences, SNPs, STRs, RFLPsM. Currat et al.
SplitsTree [48] Tree and network programComputation, visualization and exploration of phylogenetic trees and networksD.H. Huson and D. Bryant
TNT [49] Phylogenetic inferenceParsimony, weighting, ratchet, tree drift, tree fusing, sectorial searchesP. A. Goloboff, J. S. Farris, and K. C. Nixon
TOPALiPhylogenetic inferencePhylogenetic model selection, Bayesian analysis and Maximum Likelihood phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysisIain Milne, Dominik Lindner et al.
TreeGenTree construction given precomputed distance dataDistance matrixETH Zurich
TreeAlignEfficient hybrid methodDistance matrix and approximate parsimony J. Hein
TreeLineTree construction algorithm within the DECIPHER package for RMaximum likelihood, maximum parsimony, and distanceE. Wright
Treefinder [50] 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, user-definable), GUI and scripting language Maximum likelihood, distances, and othersJobb G, von Haeseler A, Strimmer K
Tree-Puzzle [51] (No longer maintained; superseded by IQ-TREE) [52] Maximum likelihood and statistical analysisMaximum likelihoodH. A. Schmidt, K. Strimmer, M. Vingron, and A. von Haeseler
T-REX (Webserver) [53] [54] Tree inference and visualization, Horizontal gene transfer detection, multiple sequence alignmentDistance (neighbor joining), Parsimony and Maximum likelihood (PhyML, RAxML) tree inference, MUSCLE, MAFFT and ClustalW sequence alignments and related applicationsBoc A, Diallo AB, Makarenkov V
UShER [55] Phylogenetic placement using maximum parsimony for viral genomesMaximum parsimonyTurakhia Y, Thornlow B, Hinrichs AS, De Maio N, Gozashti L, Lanfear R, Haussler D and Corbett-Detig R
UGENE Fast and free multiplatform tree editorGUI with PHYLIP 3.6 and IQTree algorithmsUnipro
VeryFastTree [56] A highly-tuned tool that uses parallelizing and vectorizing strategies to speed inference of phylogenies for huge alignmentsApproximate maximum likelihoodCésar Piñeiro. José M. Abuín and Juan C. Pichel
WincladaGUI and tree editor (requires Nona)Maximum parsimony, ratchetK. Nixon
Xrate Phylo-grammar engineRate estimation, branch length estimation, alignment annotationI. Holmes

See also

References

  1. ↑ Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D (November 2012). "Ancient admixture in human history". Genetics. 192 (3): 1065–93. doi:10.1534/genetics.112.145037. PMC   3522152 . PMID   22960212.
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  3. ↑ Kück P, Meid SA, Groß C, Wägele JW, Misof B (August 2014). "AliGROOVE--visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support". BMC Bioinformatics. 15 (1): 294. doi: 10.1186/1471-2105-15-294 . PMC   4167143 . PMID   25176556.
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