Biology:List of phylogenetics software

From HandWiki
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), unweighted pair group method with arithmetic mean (UPGMA), Bayesian phylogenetic inference, maximum likelihood, and distance matrix methods.

List

Name Description Methods Author
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 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[4] R-Project package for analysis of phylogenetics and evolution Provides a large variety of phylogenetics functions Maintainer: Emmanuel Paradis
Armadillo Workflow Platform[5] 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[6] Simultaneous Bayesian inference of alignment and phylogeny Bayesian inference, alignment as well as tree search M.A. Suchard, B. D. Redelings
BATWING[7] Bayesian Analysis of Trees With Internal Node Generation Bayesian inference, demographic history, population splits I. J. Wilson, Weale, D.Balding
BayesPhylogenies[8] Bayesian inference of trees using Markov chain Monte Carlo methods Bayesian 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 available Trait analysis M. Pagel, A. Meade
BEAST[10] 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[11] 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
Canopy[12] 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
CGRphylo[13] CGR method for accurate classification and tracking of rapidly evolving viruses Chaos Game Representation (CGR) method, based on concepts of statistical physics Amarinder Singh Thind, Somdatta Sinha
CITUP Clonality Inference in Tumors Using Phylogeny Exhaustive search, Quadratic Integer Programming (QIP) S. Malikic, A.W. McPherson, N. Donmez, C.S. Sahinalp
CladoGraph The main goal of Cladograph is to provide a user-friendly tool for students, teachers, and researchers to explore evolutionary relationships between different species. Trait analisys Pedro Andrade Giroldo
ClustalW Progressive multiple sequence alignment Distance matrix/nearest neighbor Thompson et al.[14]
CoalEvol Simulation 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 sequences M. Arenas, D. Posada
CodABC Coestimation of substitution, recombination and dN/dS in protein sequences Approximate Bayesian computation M. Arenas, J.S. Lopes, M.A. Beaumont, D. Posada
Dendroscope[15] Tool for visualizing rooted trees and calculating rooted networks Rooted trees, tanglegrams, consensus networks, hybridization networks Daniel 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 machines Brute force search and homotopy algorithm Jia 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 analysis Multiple sequence alignment and editing Y.-S. Jeon, K. Lee, S.-C. Park, B.-S. Kim, Y.-J. Cho, S.-M. Ha, and J. Chun
fastDNAml Optimized maximum likelihood (nucleotides only) Maximum likelihood G.J. Olsen
FastTree 2[19] 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
INDELible[20] Simulation of DNA/protein sequence evolution Simulation W. Fletcher, Z. Yang
IQPNNI (No longer maintained; superseded by IQ-TREE)[21] Iterative ML treesearch with stopping rule Maximum likelihood, neighbor-joining L.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-Puzzle Maximum likelihood, model selection, partitioning scheme finding, AIC, AICc, BIC, ultrafast bootstrapping,[24] 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[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 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[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]
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,[29] also K. Alphonse
MrBayes Posterior probability estimation Bayesian inference J. Huelsenbeck, et al.[30]
Network Free Phylogenetic Network Software Median Joining, Reduced Median, Steiner Network A. Roehl
Nona Phylogenetic inference Maximum parsimony, implied weighting, ratchet P. Goloboff
OrientAGraph Admixture graph reconstruction from allele frequencies f2-statistics or covariance matrix, maximum likelihood network orientation search implemented within TreeMix [31] Erin Molloy, Arun Durvasula, Sriram Sankararaman [32]
PAML[33] Phylogenetic analysis by maximum likelihood Maximum likelihood and Bayesian inference Z. Yang
ParaPhylo[34] Computation of gene and species trees based on event-relations (orthology, paralogy) Cograph-Editing and Triple-Inference Hellmuth
PartitionFinder[35] 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[36]
PAUP* Phylogenetic analysis using parsimony (*and other methods) Maximum parsimony, distance matrix, maximum likelihood D. Swofford
phangorn[37] Phylogenetic analysis in R ML, MP, distance matrix, bootstrap, phylogentic networks, bootstrap, model selection, SH-test, SOWH-test Maintainer: K. Schliep
Phybase[38] 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 PHYLogeny 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[39] Fast and accurate estimation of phylogenies using maximum likelihood Maximum likelihood S. Guindon & O. Gascuel
phyx[40] 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
ProtASR2[41] Ancestral reconstruction of protein sequences accounting for folding stability Maximum likelihood, substitution models M. Arenas, U. Bastolla
ProtEvol Simulation of protein sequences under structurally constrained substitution models Simulating sequences, substitution models M. Arenas, A. Sanchez-Cobos, U. Bastolla U
ProteinEvolver Simulation of protein sequences along phylogenies under empirical and structurally constrained substitution models of protein evolution Simulating sequences forward in time, substitution models M. Arenas, H.G. Dos Santos, D. Posada, U. Bastolla
ProteinEvolverABC[42] Coestimation of recombination and substitution rates in protein sequences Approximate Bayesian computation M. Arenas
ProteinModelerABC[43] Selection among site-dependent structurally constrained substitution models of protein evolution Approximate Bayesian computation D. Ferreiro et al
ProtTest3 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[44] 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
RevBayes[45] RevBayes provides an interactive environment for statistical computation in phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly phylogenetics. However, the environment is quite general and can be useful for many complex modeling tasks. Bayesian inference S. Höhna et al.[46]
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 accuracy and speed. A hybrid maximum-likelihood – neighbor-joining method M. Ninio, E. Privman, T. Pupko, N. Friedman
SGWE Simulation of genome-wide evolution along phylogenetic trees Simulating genome-wide sequences forward time Arenas M., Posada D.
SimPlot++[47] Sequence similarity plots (SimPlots[48]), detection of intragenic and intergenic recombination events, bootscan analysis[49] 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[50] Hypothesis testing SOWH test Samuel H Church, Joseph F Ryan, and Casey W Dunn
Splatche3[51] Simulation of genetic data under diverse spatially explicit evolutionary scenarios Coalescent, molecular evolution, DNA sequences, SNPs, STRs, RFLPs M. Currat et al.
SplitsTree[52] Tree and network program Computation, visualization and exploration of phylogenetic trees and networks D.H. Huson and D. Bryant
TNT[53] Phylogenetic inference Parsimony, weighting, ratchet, tree drift, tree fusing, sectorial searches P. A. Goloboff, J. S. Farris, and K. C. Nixon
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[54] 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
TreeMix Admixture graph reconstruction from allele frequencies f2-statistics or covariance matrix, maximum likelihood, heuristic search (building tree via randomized taxon addition and then adding admixture edges) Joseph K. Pickrell and Jonathan K. Pritchard [55]
Tree-Puzzle[56] (No longer maintained; superseded by IQ-TREE)[57] Maximum likelihood and statistical analysis Maximum likelihood H. A. Schmidt, K. Strimmer, M. Vingron, and A. von Haeseler
TREE-QMC Summarizes unrooted gene trees into unrooted species tree Graph-cut-based heuristic for maximum quartet support species tree problem [58][59] Yunheng Han, Erin Molloy [60][61]
T-REX (Webserver)[62][63] 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[64] 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[65] A highly-tuned tool that uses parallelizing and vectorizing strategies to speed 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

References

  1. ↑ "Ancient admixture in human history". Genetics 192 (3): 1065–93. November 2012. doi:10.1534/genetics.112.145037. PMID 22960212. 
  2. ↑ "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. 
  3. ↑ "AliGROOVE--visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support". BMC Bioinformatics 15 (1): 294. August 2014. doi:10.1186/1471-2105-15-294. PMID 25176556. 
  4. ↑ "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. 
  5. ↑ "Armadillo 1.1: an original workflow platform for designing and conducting phylogenetic analysis and simulations". PLOS One 7 (1). 2012. doi:10.1371/journal.pone.0029903. PMID 22253821. Bibcode: 2012PLoSO...729903L. 
  6. ↑ "BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny". Bioinformatics 22 (16): 2047–8. August 2006. doi:10.1093/bioinformatics/btl175. PMID 16679334. 
  7. ↑ "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. 
  8. ↑ BayesPhylogenies 1.0. Software distributed by the authors., 2007 
  9. ↑ "BayesTraits. Computer program and documentation". 2007. pp. 1216–23. http://www.evolution.rdg.ac.uk/BayesTraits. 
  10. ↑ "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. 
  11. ↑ Larget, Bret R.; Kotha, Satish K.; Dewey, Colin N.; Ané, Cécile (September 2010). "BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis". Bioinformatics 26 (22): 2910–2911. doi:10.1093/bioinformatics/btq539. PMID 20861028. 
  12. ↑ "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. Bibcode: 2016PNAS..113E5528J. 
  13. ↑ Thind, Amarinder Singh; Sinha, Somdatta (2023). "Using Chaos-Game-Representation for Analysing the SARS-CoV-2 Lineages, Newly Emerging Strains and Recombinants" (in en). Current Genomics 24 (3): 187–195. doi:10.2174/0113892029264990231013112156. PMID 38178984. PMC 10761335. https://www.eurekaselect.com/article/135525. 
  14. ↑ 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. 
  15. ↑ "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. 
  16. ↑ "Efficient Projection onto the Perfect Phylogeny Model". 2018. pp. 4108–4118. 
  17. ↑ "Exact inference under the perfect phylogeny model". 
  18. ↑ "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. 
  19. ↑ "FastTree 2--approximately maximum-likelihood trees for large alignments". PLOS One 5 (3). March 2010. doi:10.1371/journal.pone.0009490. PMID 20224823. Bibcode: 2010PLoSO...5.9490P. 
  20. ↑ Fletcher, William; Yang, Ziheng (2009-08-01). "INDELible: A Flexible Simulator of Biological Sequence Evolution". Molecular Biology and Evolution 26 (8): 1879–1888. doi:10.1093/molbev/msp098. ISSN 0737-4038. PMID 19423664. PMC 2712615. https://academic.oup.com/mbe/article/26/8/1879/980884. 
  21. ↑ "IQPNNI - Important Quartet Puzzling and Nearest Neighbor Interchange". Wien, Austria: University of Vienna. 20 August 2010. http://www.cibiv.at/software/iqpnni/. 
  22. ↑ "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. 
  23. ↑ Minh, Bui Quang; Schmidt, Heiko A; Chernomor, Olga; Schrempf, Dominik; Woodhams, Michael D; von Haeseler, Arndt; Lanfear, Robert (February 2020). "IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era". Molecular Biology and Evolution 37 (5): 1530–1534. doi:10.1093/molbev/msaa015. ISSN 0737-4038. PMID 32011700. 
  24. ↑ "Ultrafast approximation for phylogenetic bootstrap". Molecular Biology and Evolution 30 (5): 1188–95. May 2013. doi:10.1093/molbev/mst024. PMID 23418397. 
  25. ↑ "A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies". Research Ideas and Outcomes 5. June 2019. doi:10.3897/rio.5.e36178. 
  26. ↑ "On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference". F1000Research 9: 1309. November 2020. doi:10.12688/f1000research.26930.1. PMID 33335719. 
  27. ↑ Campbell, Ellsworth M.; Boyles, Anthony; Shankar, Anupama; Kim, Jay; Knyazev, Sergey; Cintron, Roxana; Switzer, William M. (2021-09-07). "MicrobeTrace: Retooling molecular epidemiology for rapid public health response" (in en). PLOS Computational Biology 17 (9). doi:10.1371/journal.pcbi.1009300. ISSN 1553-7358. PMID 34492010. Bibcode: 2021PLSCB..17E9300C. 
  28. ↑ Haschka, Thomas; Ponger, Loic; Escudé, Christophe; Mozziconacci, Julien (2021-06-08). "MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences". Bioinformatics 37 (21): 3947–3949. doi:10.1093/bioinformatics/btab430. ISSN 1367-4803. PMID 34100911. 
  29. ↑ 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. PMID 34875801. 
  30. ↑ 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. 
  31. ↑ Pickrell, Joseph K.; Pritchard, Jonathan K. (15 November 2012). "Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data". PLOS Genetics 8 (11). doi:10.1371/journal.pgen.1002967. PMID 23166502. 
  32. ↑ Molloy, Erin K; Durvasula, Arun; Sankararaman, Sriram (12 July 2021). "Advancing admixture graph estimation via maximum likelihood network orientation". Bioinformatics 37 (Supplement_1): i142–i150. doi:10.1093/bioinformatics/btab267. 
  33. ↑ Yang, Ziheng (May 2007). "PAML 4: Phylogenetic Analysis by Maximum Likelihood". Molecular Biology and Evolution 24 (8): 1586–1591. doi:10.1093/molbev/msm088. ISSN 0737-4038. PMID 17483113. 
  34. ↑ "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. 
  35. ↑ Lanfear, Robert; Frandsen, Paul B; Wright, April M; Senfeld, Tereza; Calcott, Brett (24 December 2016). "PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses". Molecular Biology and Evolution 34 (3): 772–773. doi:10.1093/molbev/msw260. ISSN 0737-4038. PMID 28013191. 
  36. ↑ 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. Bibcode: 2013MEcEv...4.1011T. 
  37. ↑ "phangorn: phylogenetic analysis in R". Bioinformatics 27 (4): 592–3. February 2011. doi:10.1093/bioinformatics/btq706. PMID 21169378. 
  38. ↑ "Phybase: an R package for species tree analysis". Bioinformatics 26 (7): 962–3. April 2010. doi:10.1093/bioinformatics/btq062. PMID 20156990. 
  39. ↑ Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent; Anisimova, Maria; Hordijk, Wim; Gascuel, Olivier (2010-03-29). "New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0". Systematic Biology 59 (3): 307–321. doi:10.1093/sysbio/syq010. ISSN 1076-836X. PMID 20525638. 
  40. ↑ "Phyx: phylogenetic tools for unix". Bioinformatics 33 (12): 1886–1888. June 2017. doi:10.1093/bioinformatics/btx063. PMID 28174903. 
  41. ↑ Arenas, Miguel; Bastolla, Ugo (2020). "ProtASR2: Ancestral reconstruction of protein sequences accounting for folding stability" (in en). Methods in Ecology and Evolution 11 (2): 248–257. doi:10.1111/2041-210X.13341. ISSN 2041-210X. Bibcode: 2020MEcEv..11..248A. https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13341. 
  42. ↑ Arenas, Miguel (2021-08-27). "ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation". Bioinformatics 38 (1): 58–64. doi:10.1093/bioinformatics/btab617. ISSN 1367-4803. PMID 34450622. 
  43. ↑ Ferreiro, David; Branco, Catarina; Arenas, Miguel (2024). "Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation". Bioinformatics 40 (3). doi:10.1093/bioinformatics/btae096. ISSN 1367-4811. PMID 38374231. PMC 10914458. https://academic.oup.com/bioinformatics/article/40/3/btae096/7610882. 
  44. ↑ "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. 
  45. ↑ Höhna, Sebastian; Landis, Michael J.; Heath, Tracy A.; Boussau, Bastien; Lartillot, Nicolas; Moore, Brian R.; Huelsenbeck, John P.; Ronquist, Fredrik (July 2016). "RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language" (in en). Systematic Biology 65 (4): 726–736. doi:10.1093/sysbio/syw021. ISSN 1063-5157. PMID 27235697. PMC 4911942. https://academic.oup.com/sysbio/article-lookup/doi/10.1093/sysbio/syw021. 
  46. ↑ "revbayes" (in en). https://github.com/revbayes. 
  47. ↑ Samson, Stéphane; Lord, Étienne; Makarenkov, Vladimir (26 May 2022). "SimPlot++: a Python application for representing sequence similarity and detecting recombination". Bioinformatics 38 (11): 3118–3120. doi:10.1093/bioinformatics/btac287. PMID 35451456. 
  48. ↑ Lole, Kavita S.; Bollinger, Robert C.; Paranjape, Ramesh S.; Gadkari, Deepak; Kulkarni, Smita S.; Novak, Nicole G.; Ingersoll, Roxann; Sheppard, Haynes W. et al. (January 1999). "Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination". Journal of Virology 73 (1): 152–160. doi:10.1128/JVI.73.1.152-160.1999. PMID 9847317. 
  49. ↑ Salminen, Mika O.; Carr, Jean K.; Burke, Donald S.; McCutchan, Francine E. (November 1995). "Identification of Breakpoints in Intergenotypic Recombinants of HIV Type 1 by Bootscanning". AIDS Research and Human Retroviruses 11 (11): 1423–1425. doi:10.1089/aid.1995.11.1423. PMID 8573403. 
  50. ↑ "Automation and Evaluation of the SOWH Test with SOWHAT". Systematic Biology 64 (6): 1048–58. November 2015. doi:10.1093/sysbio/syv055. PMID 26231182. 
  51. ↑ Currat, Mathias; Arenas, Miguel; Quilodràn, Claudio S; Excoffier, Laurent; Ray, Nicolas (2019-05-11). "SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal". Bioinformatics 35 (21): 4480–4483. doi:10.1093/bioinformatics/btz311. ISSN 1367-4803. PMID 31077292. 
  52. ↑ "Application of phylogenetic networks in evolutionary studies". Molecular Biology and Evolution 23 (2): 254–67. February 2006. doi:10.1093/molbev/msj030. PMID 16221896. 
  53. ↑ Goloboff, Pablo A.; Farris, James S.; Nixon, Kevin C. (29 September 2008). "TNT, a free program for phylogenetic analysis". Cladistics 24 (5): 774–786. doi:10.1111/j.1096-0031.2008.00217.x. https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1096-0031.2008.00217.x. 
  54. ↑ "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.  (Retracted, see doi:10.1186/s12862-015-0513-z, PMID 26542699,  Retraction Watch)
  55. ↑ Pickrell, Joseph K.; Pritchard, Jonathan K. (15 November 2012). "Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data". PLOS Genetics 8 (11). doi:10.1371/journal.pgen.1002967. PMID 23166502. 
  56. ↑ "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. 
  57. ↑ "iqtree2". https://github.com/iqtree/iqtree2. 
  58. ↑ Snir, Sagi; Rao, Satish (1 January 2012). "Quartet MaxCut: A fast algorithm for amalgamating quartet trees". Molecular Phylogenetics and Evolution 62 (1): 1–8. doi:10.1016/j.ympev.2011.06.021. PMID 21762785. Bibcode: 2012MolPE..62....1S. 
  59. ↑ Avni, Eliran; Cohen, Reuven; Snir, Sagi (1 March 2015). "Weighted Quartets Phylogenetics". Systematic Biology 64 (2): 233–242. doi:10.1093/sysbio/syu087. PMID 25414175. 
  60. ↑ Han, Yunheng; Molloy, Erin K (25 February 2025). "Improved robustness to gene tree incompleteness, estimation errors, and systematic homology errors with weighted TREE-QMC". Systematic Biology. doi:10.1093/sysbio/syaf009. PMID 40000439. 
  61. ↑ Han, Yunheng; Molloy, Erin K. (1 July 2023). "Improving quartet graph construction for scalable and accurate species tree estimation from gene trees". Genome Research 33 (7): 1042–1052. doi:10.1101/gr.277629.122. PMID 37197990. 
  62. ↑ "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. 
  63. ↑ "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. 
  64. ↑ "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. 
  65. ↑ Piñeiro, César; Abuín, José M; Pichel, Juan C (2020-11-01). Ponty, Yann. ed. "Very Fast Tree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies" (in en). Bioinformatics 36 (17): 4658–4659. doi:10.1093/bioinformatics/btaa582. ISSN 1367-4803. PMID 32573652. https://academic.oup.com/bioinformatics/article/36/17/4658/5861530. 



Retrieved from "https://handwiki.org/wiki/index.php?title=Biology:List_of_phylogenetics_software&oldid=4040611"