List of phylogenetics software

Short description: Compilation of software used to produce phylogenetic trees

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

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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, 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 [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.[11]
Dendroscope[12] | Tool for visualizing rooted trees and calculating rooted networks | Rooted trees, tanglegrams, consensus networks, hybridization networks | Daniel Huson et al.
EzEditor [13] | 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[14] | 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 [15] | 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,[16] 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
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
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,[17] also K. Alphonse
MrBayes  | Posterior probability estimation | Bayesian inference | J. Huelsenbeck, et al.[18]
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 [19] | 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[20]
PAUP* | Phylogenetic analysis using parsimony (*and other methods) | Maximum parsimony, distance matrix, maximum likelihood | D. Swofford
phangorn [21] | Phylogenetic analysis in R | ML, MP, distance matrix, bootstrap, phylogentic networks, bootstrap, model selection, SH-test, SOWH-test | Maintainer: K. Schliep
Phybase[22] | 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 [23] | 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 [24] | 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 [25] | Hypothesis testing | SOWH test | Church, Ryan, and Dunn
SplitsTree[26] | 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[27] | 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 [28][29] | Maximum likelihood and statistical analysis | Maximum likelihood | Makarenkov
T-REX (Webserver)[30] | 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 [31] | 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 | 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

## See also

* List of phylogenetic tree visualization software

## References

1. ↑ "Reconstruction of clonal trees and tumor composition from multi-sample sequencing data". Bioinformatics 31 (12): i62-70. June 2015. doi:10.1093/bioinformatics/btv261. PMID 26072510.
2. ↑ "AliGROOVE--visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support". BMC Bioinformatics 15: 294. August 2014. doi:10.1186/1471-2105-15-294. PMID 25176556.
3. ↑ "APE: Analyses of Phylogenetics and Evolution in R language". Bioinformatics (Oxford, England) 20 (2): 289–90. January 2004. doi:10.1093/bioinformatics/btg412. PMID 14734327.
4. ↑ "Armadillo 1.1: an original workflow platform for designing and conducting phylogenetic analysis and simulations". PLOS ONE 7 (1): e29903. 2012. doi:10.1371/journal.pone.0029903. PMID 22253821. Bibcode: 2012PLoSO...729903L.
5. ↑ "BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny". Bioinformatics 22 (16): 2047–8. August 2006. doi:10.1093/bioinformatics/btl175. PMID 16679334.
6. ↑ "Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities.". Journal of the Royal Statistical Society, Series A (Statistics in Society) 166 (2): 155–88. June 2003. doi:10.1111/1467-985X.00264.
7. ↑ BayesPhylogenies 1.0. Software distributed by the authors., 2007
8. ↑ "BayesTraits. Computer program and documentation". 2007. pp. 1216–23. http://www.evolution.rdg.ac.uk/BayesTraits.
9. ↑ "Bayesian phylogenetics with BEAUti and the BEAST 1.7". Molecular Biology and Evolution 29 (8): 1969–1973. 2012. doi:10.1093/molbev/mss075. PMID 22367748.
10. ↑ "Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing". Proceedings of the National Academy of Sciences of the United States of America 113 (37): E5528-37. September 2016. doi:10.1073/pnas.1522203113. PMID 27573852.
11. ↑ Thompson, Julie D.; Gibson, Toby J.; Higgins, Des G. (August 2002). "Multiple sequence alignment using ClustalW and ClustalX". Current Protocols in Bioinformatics Chapter 2: 2.3.1–2.3.22. doi:10.1002/0471250953.bi0203s00. ISSN 1934-340X. PMID 18792934.
12. ↑ "Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks". Systematic Biology 61 (6): 1061–7. December 2012. doi:10.1093/sysbio/sys062. PMID 22780991.
13. ↑ "EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes". International Journal of Systematic and Evolutionary Microbiology 64 (Pt 2): 689–91. February 2014. doi:10.1099/ijs.0.059360-0. PMID 24425826.
14. ↑ "FastTree 2--approximately maximum-likelihood trees for large alignments". PLOS ONE 5 (3): e9490. March 2010. doi:10.1371/journal.pone.0009490. PMID 20224823. Bibcode: 2010PLoSO...5.9490P.
15. ↑ "IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies". Molecular Biology and Evolution 32 (1): 268–74. January 2015. doi:10.1093/molbev/msu300. PMID 25371430.
16. ↑ "Ultrafast approximation for phylogenetic bootstrap". Molecular Biology and Evolution 30 (5): 1188–95. May 2013. doi:10.1093/molbev/mst024. PMID 23418397.
17. ↑ O’Leary, Maureen A.; Kaufman, Seth (October 2011). "MorphoBank: phylophenomics in the "cloud"" (in en). Cladistics 27 (5): 529–537. doi:10.1111/j.1096-0031.2011.00355.x. http://doi.wiley.com/10.1111/j.1096-0031.2011.00355.x.
18. ↑ Huelsenbeck, J. P.; Ronquist, F. (August 2001). "MRBAYES: Bayesian inference of phylogenetic trees". Bioinformatics 17 (8): 754–755. doi:10.1093/bioinformatics/17.8.754. ISSN 1367-4803. PMID 11524383.
19. ↑ "Phylogenomics with paralogs". Proceedings of the National Academy of Sciences of the United States of America 112 (7): 2058–63. February 2015. doi:10.1073/pnas.1412770112. PMID 25646426. Bibcode: 2015PNAS..112.2058H.
20. ↑ Thomas, Gavin H.; Hartmann, Klaas; Jetz, Walter; Joy, Jeffrey B.; Mimoto, Aki; Mooers, Arne O. (2013). "PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences" (in en). Methods in Ecology and Evolution 4 (11): 1011–1017. doi:10.1111/2041-210X.12117. ISSN 2041-210X.
21. ↑ "phangorn: phylogenetic analysis in R". Bioinformatics 27 (4): 592–3. February 2011. doi:10.1093/bioinformatics/btq706. PMID 21169378.
22. ↑ "Phybase: an R package for species tree analysis". Bioinformatics 26 (7): 962–3. April 2010. doi:10.1093/bioinformatics/btq062. PMID 20156990.
23. ↑ "Phyx: phylogenetic tools for unix". Bioinformatics 33 (12): 1886–1888. June 2017. doi:10.1093/bioinformatics/btx063. PMID 28174903.
24. ↑ "RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference". Bioinformatics 35 (21): 4453–4455. May 2019. doi:10.1093/bioinformatics/btz305. PMID 31070718.
25. ↑ "Automation and Evaluation of the SOWH Test with SOWHAT". Systematic Biology 64 (6): 1048–58. November 2015. doi:10.1093/sysbio/syv055. PMID 26231182.
26. ↑ "Application of phylogenetic networks in evolutionary studies". Molecular Biology and Evolution 23 (2): 254–67. February 2006. doi:10.1093/molbev/msj030. PMID 16221896.
27. ↑ "TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics". BMC Evolutionary Biology 4: 18. June 2004. doi:10.1186/1471-2148-4-18. PMID 15222900.
28. ↑ "T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks". Bioinformatics 17 (7): 664–8. July 2001. doi:10.1093/bioinformatics/17.7.664. PMID 11448889.
29. ↑ "TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing". Bioinformatics 18 (3): 502–4. March 2002. doi:10.1093/bioinformatics/18.3.502. PMID 11934758.
30. ↑ "T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks". Nucleic Acids Research 40 (Web Server issue): W573–9. July 2012. doi:10.1093/nar/gks485. PMID 22675075.
31. ↑ "Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic". Nature Genetics 53 (6): 809–816. June 2021. doi:10.1038/s41588-021-00862-7. PMID 33972780.

## 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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Phylogenetics

Relevant fields|

* Computational phylogenetics
* Molecular phylogenetics
* Cladistics
* Taxonomy
* Evolutionary taxonomy
* Systematics

Note: This topic belongs to "Evolutionary biology" portal

Basic concepts|

* Phylogenesis
* Cladogenesis
* Phylogenetic tree
* Cladogram
* Phylogenetic network
* Long branch attraction
* Clade vs Grade
* Lineage
* Ghost lineage
* Ghost population

Inference methods|

* Maximum parsimony
* Probabilistic methods
* Maximum likelihood
* Bayesian inference
* Distance-matrix methods
* Neighbor-joining
* UPGMA
* Least squares
* Three-taxon analysis

Current topics|

* PhyloCode
* DNA barcoding
* Molecular phylogenetics
* Phylogenetic comparative methods
* Phylogenetic niche conservatism
* Phylogenetics software
* Phylogenomics
* Phylogeography

Group traits|

* Primitive
* Plesiomorphy
* Symplesiomorphy
* Derived
* Apomorphy
* Synapomorphy
* Autapomorphy

Group types|

* Monophyly
* Paraphyly
* Polyphyly

Nomenclature|

* Phylogenetic nomenclature
* Crown group
* Sister group
* Basal
* Supertree

* Category
* Commons

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