User:Surjray/sandbox list tools

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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.

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 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, 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[3] Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing Maximum Likelihood, Markov Chain Monte Carlo (MCMC) methods, Importance sampling 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 [4] Tool for visualizing rooted trees and calculating rooted networks Rooted trees, tanglegrams, consensus networks, hybridization networks Daniel Huson et al.
EXACT[5] Exact inference of phylogenetic trees under the perfect phylogeny model Exhaustive search, Bayesian inference, Maximum Likelihood, distributed computing S. Ray, B. Jia, S. Safavi, Tv. Opijnen, R. Isberg, J. Rosch, and J. Bento
EzEditor [6] 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[7] 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[8] 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,[9] 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[10] Computation of gene and species trees based on event-relations (orthology, paralogy) Cograph-Editing and Triple-Inference 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 [11] Phylogenetic analysis in R ML, MP, distance matrix, bootstrap, phylogentic networks, bootstrap, model selection, SH-test, SOWH-test Maintainer: K. Schliep
Phybase [12] 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 Markov chain Monte Carlo 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 [13] 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 [14] 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 [15] Hypothesis testing SOWH test Church, Ryan, and Dunn
SplitsTree [16] 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, user-definable), GUI and scripting language Maximum likelihood, distances, and others G. Jobb
TREE-PUZZLE Maximum likelihood and statistical analysis Maximum likelihood H.A. Schmidt, K. Strimmer, A. von Haeseler
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 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 Phylo-grammar engine Rate estimation, branch length estimation, alignment annotation I. Holmes

See also[edit]

References[edit]

  1. ^ El-Kebir, Mohammed; Oesper, Layla; Acheson-Field, Hannah; Raphael, Benjamin J. (2015-06-15). "Reconstruction of clonal trees and tumor composition from multi-sample sequencicanng data". Bioinformatics. 31 (12): i62–i70. doi:10.1093/bioinformatics/btv261. ISSN 1367-4803. PMC 4542783. PMID 26072510.{{cite journal}}: CS1 maint: PMC format (link)
  2. ^ AliGROOVE - visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support; Kueck et al.;BMC Bioinformatics 2014; 15:294
  3. ^ Jiang, Yuchao; Qiu, Yu; Minn, Andy J.; Zhang, Nancy R. (2016-09-13). "Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing". Proceedings of the National Academy of Sciences. 113 (37): E5528–E5537. doi:10.1073/pnas.1522203113. ISSN 0027-8424. PMC 5027458. PMID 27573852.{{cite journal}}: CS1 maint: PMC format (link)
  4. ^ 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
  5. ^ Ray, Surjyendu; Jia, Bei; Safavi, Sam; van Opijnen, Tim; Isberg, Ralph; Rosch, Jason; Bento, José (2019-08-22). "Exact inference under the perfect phylogeny model". {{cite journal}}: Cite journal requires |journal= (help)
  6. ^ Yoon-Seong Jeon, Kihyun Lee, Sang-Cheol Park, Bong-Soo Kim, Yong-Joon Cho, Sung-Min Ha and Jongsik Chun, 10.1099/ijs.0.059360-0 IJSEM December 2013 Int J Syst Evol Microbiol 64, 689-691
  7. ^ Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.; Poon, Art F. Y. (10 March 2010). "FastTree 2 - Approximately Maximum-Likelihood Trees for Large Alignments". PLoS ONE. 5 (3): e9490. doi:10.1371/journal.pone.0009490. PMC 2835736. PMID 20224823.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  8. ^ Nguyen, Lam-Tung; Chernomor, O; Schmidt, HA; von Haeseler, A; Minh, BQ (Jan 2015). "IQ-TREE: 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.
  9. ^ 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.
  10. ^ Phylogenomics with paralogs; Hellmuth et al.; Proc Natl Acad Sci 2015; 112:7
  11. ^ Schliep, KP (2011). "phangorn: phylogenetic analysis in R". Bioinformatics. 27 (4): 592–593. doi:10.1093/bioinformatics/btq706. PMC 3035803. PMID 21169378.
  12. ^ Liu L., Yu L. (2010). "an R package for species tree analysis". Bioinformatics. 26 (7): 962–963. doi:10.1093/bioinformatics/btq062. PMID 20156990.
  13. ^ Brown, JW; Walker, JF; Smith, SA (2017). "Phyx: phylogenetic tools for unix". Bioinformatics. 33 (12): 1886–1888. doi:10.1093/bioinformatics/btx063. PMC 5870855. PMID 28174903.
  14. ^ Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. "RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference". doi:10.1093/bioinformatics/btz305. {{cite journal}}: Cite journal requires |journal= (help)
  15. ^ 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.
  16. ^ 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[edit]


Category:Computational phylogenetics Phylogenetics Category:Bioinformatics software Category:Phylogenetics

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