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Phylogenetics
List of phylogenetics software
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    List of phylogenetics software

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    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), UPGMA, Bayesian phylogenetic inference, maximum likelihood and distance matrix methods.

    List

    Name Description Methods Author
    ADMIXTOOLS R software package that contains the qpGraph, qpAdm, qpWave, and qpDstat programs Nick Patterson and David Reich
    AncesTree 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, and B. J. Raphael
    AliGROOVE 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 R-Project 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
    BAli-Phy 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 (auto-partitioning) 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, 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 data. Neighbor-joining, 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 & tree-puzzle) 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
    Canopy Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing Maximum Likelihood, Markov Chain Monte Carlo (MCMC) methods Y. Jiang, Y. Qiu, A. J. Minn, and N. R. Zhang
    CITUP Clonality Inference in Tumors Using Phylogeny Exhaustive search, Quadratic Integer Programming (QIP) S. Malikic, A.W. McPherson, N. Donmez, C.S. Sahinalp
    ClustalW Progressive multiple sequence alignment Distance matrix/nearest neighbor Thompson et al.
    Dendroscope Tool for visualizing rooted trees and calculating rooted networks Rooted trees, tanglegrams, consensus networks, hybridization networks Daniel Huson et al.
    EXACT
    EzEditor 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 analysis. Neighbor Joining Jeon, Y.S. et al.
    fastDNAml Optimized maximum likelihood (nucleotides only) Maximum likelihood G.J. Olsen
    FastTree 2 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 branch-site 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 Neighbor-joining, UPGMA, MrBayes plugin, PHYML plugin, RAxML plugin, FastTree plugin, GARLi plugin, PAUP* Plugin A. J. Drummond,M.Suchard,V.Lefort et al.
    Genozip Genozip is a compressor of FASTA and PHYLIP files (as well as FASTQ, BAM, VCF etc), and it can also convert MultiFASTA to PHYLIP and vice versa. Lan, Divon et al.
    HyPhy Hypothesis testing using phylogenies Maximum likelihood, neighbor-joining, clustering techniques, distance matrices S.L. Kosakovsky Pond, S.D.W. Frost, S.V. Muse
    IQPNNI Iterative ML treesearch with stopping rule Maximum likelihood, neighbor-joining L.S. Vinh, A. von Haeseler, B.Q. Minh
    IQ-TREE An efficient phylogenomic software by maximum likelihood, as successor of IQPNNI and TREE-PUZZLE. Maximum likelihood, model selection, partitioning scheme finding, AIC, AICc, BIC, ultrafast bootstrapping, branch tests, tree topology tests, likelihood mapping Lam-Tung Nguyen, O. Chernomor, H.A. Schmidt, A. von Haeseler, B.Q. Minh
    jModelTest 2 A high-performance computing program to carry out statistical selection of best-fit models of nucleotide substitution Maximum likelihood, AIC, BIC, DT, hLTR, dLTR D. Darriba, GL. Taboada, R. Doallo, D. Posada
    JolyTree 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 Quartets A. Criscuolo
    LisBeth Three-item analysis for phylogenetics and biogeography Three-item analysis J. Ducasse, N. Cao & R. Zaragüeta-Bagils
    MEGA Molecular Evolutionary Genetics Analysis Distance, Parsimony and Maximum Composite Likelihood Methods Tamura K, Dudley J, Nei M & Kumar S
    MegAlign Pro MegAlign 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
    MetaPIGA2 Maximum 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 testing. Michel 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
    Modelgenerator Model selection (protein or nucleotide) Maximum likelihood Thomas Keane
    MOLPHY Molecular phylogenetics (protein or nucleotide) Maximum likelihood J. Adachi and M. Hasegawa
    MorphoBank Web application to organize trait data (morphological characters) for tree building for use with Maximum Parsimony (via the CIPRES portal), Maximum Likelihood, and Bayesian analysis) O'Leary, M. A., and S. Kaufman, also K. Alphonse
    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 Computation of gene and species trees based on event-relations (orthology, paralogy) Cograph-Editing and Triple-Inference Hellmuth
    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
    PASTIS R package for phylogenetic assembly R, two‐stage Bayesian inference using MrBayes 3.2 Thomas et al. 2013
    PAUP* Phylogenetic analysis using parsimony (*and other methods) Maximum parsimony, distance matrix, maximum likelihood D. Swofford
    phangorn Phylogenetic analysis in R ML, MP, distance matrix, bootstrap, phylogentic networks, bootstrap, model selection, SH-test, SOWH-test Maintainer: K. Schliep
    Phybase 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 Wei-Chen 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
    PhyloWGS Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors MCMC A. G. Deshwar, S. Vembu, C. K. Yung, G. H. Jang, L. Stein, and Q. Morris
    PhyML Fast and accurate estimation of phylogenies using maximum likelihood Maximum likelihood S. Guindon & O. Gascuel
    phyx Unix/Linux command line phylogenetic tools Explore, manipulate, analyze, and simulate phylogenetic objects (alignments, trees, and MCMC logs) J.W. Brown, J.F. Walker, and S.A. Smith
    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 high-performance 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 Neighbor-joining K. Howe, A. Bateman, R. Durbin
    RAxML-HPC Randomized Axelerated Maximum Likelihood for High Performance Computing (nucleotides and aminoacids) Maximum likelihood, simple Maximum parsimony A. Stamatakis
    RAxML-NG Randomized Axelerated Maximum Likelihood for High Performance Computing (nucleotides and aminoacids) Next Generation Maximum likelihood, simple Maximum parsimony A. Kozlov, D. Darriba, T. Flouri, B. Morel, A. Stamatakis
    SEMPHY Tree 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 both accuracy and speed. A hybrid maximum-likelihood / neighbor-joining method M. Ninio, E. Privman, T. Pupko, N. Friedman
    SimPlot++ Sequence similarity plots (SimPlots), detection of intragenic and intergenic recombination events, bootscan analysis and sequence similarity networks. SimPlot using different nucleotide/protein distance models; Phi, χ2 and NSS recombination tests; Sequence similarity network analysis S. Samson, E. Lord, V. Makarenkov
    sowhat Hypothesis testing SOWH test Church, Ryan, and Dunn
    SplitsTree 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
    TreeLine Tree construction algorithm within the DECIPHER package for R Maximum likelihood, maximum parsimony, and distance E. Wright
    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, user-definable), GUI and scripting language Maximum likelihood, distances, and others Jobb G, von Haeseler A, Strimmer K
    TREE-PUZZLE Maximum likelihood and statistical analysis Maximum likelihood Makarenkov
    T-REX (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 Boc A, Diallo AB, Makarenkov V
    UShER Phylogenetic placement using maximum parsimony for viral genomes Maximum parsimony Turakhia Y, Thornlow B, Hinrichs AS, De Maio N, Gozashti L, Lanfear R, Haussler D and Corbett-Detig R
    UGENE Fast and free multiplatform tree editor GUI with Phylip 3.6 and IQTree algorithms Unipro
    VeryFastTree A highly-tuned tool that takes advantage of parallelization and vectorization strategies to speed up the inference of phylogenies for huge alignments. Approximate maximum likelihood César Piñeiro. José M. Abuín and Juan C. Pichel
    Winclada GUI and tree editor (requires Nona) Maximum parsimony, ratchet K. Nixon
    Xrate Phylo-grammar engine Rate estimation, branch length estimation, alignment annotation I. Holmes

    See also

    External links


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