# List of phylogenetics software

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.

Name | Description | Methods | Author |
---|---|---|---|

AncesTree [1] | 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 [2] | 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 [3] | R-Project package for analysis of phylogenetics and evolution | Provides a large variety of phylogenetics functions | Maintainer: Emmanuel Paradis |

Armadillo Workflow Platform [4] | 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 [5] | Simultaneous Bayesian inference of alignment and phylogeny | Bayesian inference, alignment as well as tree search. | M.A. Suchard, B. D. Redelings |

BATWING [6] | Bayesian Analysis of Trees With Internal Node Generation | Bayesian inference, demographic history, population splits | I. J. Wilson, Weale, D.Balding |

BayesPhylogenies [7] | Bayesian inference of trees using Markov chain Monte Carlo methods | Bayesian inference, multiple models, mixture model (auto-partitioning) | M. Pagel, A. Meade |

BayesTraits [8] | Analyses trait evolution among groups of species for which a phylogeny or sample of phylogenies is available | Trait analysis | M. Pagel, A. Meade |

BEAST [9] | 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. | 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 [10] | 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 [11] | Tool for visualizing rooted trees and calculating rooted networks | Rooted trees, tanglegrams, consensus networks, hybridization networks | Daniel Huson et al. |

EzEditor [12] | 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[13] | 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. |

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 [14] | 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,[15] 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 |

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 |

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 |

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 [16] | 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 |

PAUP* | Phylogenetic analysis using parsimony (*and other methods) | Maximum parsimony, distance matrix, maximum likelihood | D. Swofford |

phangorn [17] | Phylogenetic analysis in R | ML, MP, distance matrix, bootstrap, phylogentic networks, bootstrap, model selection, SH-test, SOWH-test | Maintainer: K. Schliep |

Phybase [18] | 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 [19] | Unix/GNU/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 [20] | 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 |

sowhat [21] | Hypothesis testing | SOWH test | Church, Ryan, and Dunn |

SplitsTree [22] | 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 [23] | 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 [24][25] | Maximum likelihood and statistical analysis | Maximum likelihood | Makarenkov |

T-REX (Webserver) [26] | 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 |

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 | Phylo-grammar engine | Rate estimation, branch length estimation, alignment annotation | I. Holmes |

## References

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## 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

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