4121:
3798:
4133:
647:
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
629:
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
1305:
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),
414:
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
671:
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.
1138:
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 SEMPHY has become outdated.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
136:
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
262:
Neighbor-joining, maximum parsimony, UPGMA, maximum likelihood, distance matrix methods,... Calculation of the reliability of trees/branches using bootstrapping, permutation resampling or error resampling
562:
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
2672:
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".
1244:
Phylogenetic model selection, Bayesian analysis and
Maximum Likelihood phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysis
998:
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
3109:
Lole, Kavita S.; Bollinger, Robert C.; Paranjape, Ramesh S.; Gadkari, Deepak; Kulkarni, Smita S.; Novak, Nicole G.; Ingersoll, Roxann; Sheppard, Haynes W.; Ray, Stuart C. (January 1999).
3158:
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".
2073:
Jia B, Ray S, Safavi S, Bento J (2018). "Efficient
Projection onto the Perfect Phylogeny Model". In Bengio S, Wallach H, Larochelle H, Grauman K, Cesa-Bianchi N, Garnett R (eds.).
429:
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
613:'s Lasergene Molecular Biology package. This application performs multiple and pairwise sequence alignments, provides alignment editing, and generates phylogenetic trees.
3064:
Samson, Stéphane; Lord, Étienne; Makarenkov, Vladimir (26 May 2022). "SimPlot++: a Python application for representing sequence similarity and detecting recombination".
2113:
Jeon YS, Lee K, Park SC, Kim BS, Cho YJ, Ha SM, Chun J (February 2014). "EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes".
535:
Maximum likelihood, model selection, partitioning scheme finding, AIC, AICc, BIC, ultrafast bootstrapping, branch tests, tree topology tests, likelihood mapping
3400:
273:
Integrated graphical software to perform phylogenetic analyses, from the importing of sequences to the plotting and graphical edition of trees and alignments
688:
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.
3111:"Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination"
1169:
Sequence similarity plots (SimPlots), detection of intragenic and intergenic recombination events, bootscan analysis and sequence similarity networks
1447:
259:
Universal platform for the management, storage and analysis of all types of biological data, including tree and network inference of sequence data
1085:
Simulating sequences, alignment, controlling third party applications, workflows, querying databases, generating graphics and phylogenetic trees
655:, metapopulation genetic algorithm, simulated annealing, etc.), discrete Gamma rate heterogeneity, ancestral state reconstruction, model testing
590:
1566:"AliGROOVE--visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support"
1356:), Parsimony and Maximum likelihood (PhyML, RAxML) tree inference, MUSCLE, MAFFT and ClustalW sequence alignments and related applications
2399:
Campbell, Ellsworth M.; Boyles, Anthony; Shankar, Anupama; Kim, Jay; Knyazev, Sergey; Cintron, Roxana; Switzer, William M. (2021-09-07).
1040:
Simulation of protein sequences along phylogenies under empirical and structurally constrained substitution models of protein evolution
3669:
4174:
3619:"Very Fast Tree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies"
1172:
SimPlot using different nucleotide/protein distance models; Phi, χ2 and NSS recombination tests; Sequence similarity network analysis
877:
619:
610:
1871:"Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing"
307:
Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing
2960:"ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation"
3736:
1068:
A high-performance computing program for selecting the model of protein evolution that best fits a given set of aligned sequences
3244:"SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal"
1985:
Thompson, Julie D.; Gibson, Toby J.; Higgins, Des G. (August 2002). "Multiple sequence alignment using
ClustalW and ClustalX".
133:
Visualisation of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support
1399:
A highly-tuned tool that uses parallelizing and vectorizing strategies to speed inference of phylogenies for huge alignments
568:-based pairwise genome distance, Balanced Minimum Evolution (BME), ratchet-based BME tree search, Rate of Elementary Quartets
168:
Inference of phylogenetic trees using
Distance, Maximum Likelihood, Maximum Parsimony, Bayesian methods and related workflows
2813:
Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent; Anisimova, Maria; Hordijk, Wim; Gascuel, Olivier (2010-03-29).
2350:"On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference"
3931:
2309:"A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies"
1001:
Maximum parsimony, Maximum likelihood, Chromosome rearrangement, discreet characters, continuous characters, Alignment
3891:
546:
A high-performance computing program to carry out statistical selection of best-fit models of nucleotide substitution
1124:
Randomized
Axelerated Maximum Likelihood for High Performance Computing (nucleotides and aminoacids) Next Generation
675:
Ellsworth M. Campbell, Anthony Boyles, Anupama
Shankar, Jay Kim, Sergey Knyazev, Roxana Cintron, William M. Switzer
3971:
3568:"Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic"
368:
Simulation of DNA and protein evolution along phylogenetic trees (that can also be simulated with the coalescent)
4169:
4159:
3976:
3909:
1658:"Armadillo 1.1: an original workflow platform for designing and conducting phylogenetic analysis and simulations"
1466:
Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D (November 2012).
56:
3566:
Turakhia Y, Thornlow B, Hinrichs AS, De Maio N, Gozashti L, Lanfear R, Haussler D, Corbett-Detig R (June 2021).
1930:"Using Chaos-Game-Representation for Analysing the SARS-CoV-2 Lineages, Newly Emerging Strains and Recombinants"
491:
Neighbor-joining, UPGMA, MrBayes plugin, PhyML plugin, RAxML plugin, FastTree plugin, GARLi plugin, PAUP* Plugin
4137:
3916:
2815:"New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0"
64:
685:
MNHN-Tree-Tools is an opensource phylogenetics inference software working on nucleic and protein sequences.
227:
Analyses trait evolution among groups of species for which a phylogeny or sample of phylogenies is available
822:
Combined selection of models of molecular evolution and partitioning schemes for DNA and protein alignments
2912:
4164:
3896:
3803:
3759:
3729:
1760:"Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities"
474:
Fits branch-site codon models without the need of prior knowledge of clades undergoing positive selection
24:
3699:
869:
ML, MP, distance matrix, bootstrap, phylogentic networks, bootstrap, model selection, SH-test, SOWH-test
105:
3242:
Currat, Mathias; Arenas, Miguel; Quilodràn, Claudio S; Excoffier, Laurent; Ray, Nicolas (2019-05-11).
1373:
Turakhia Y, Thornlow B, Hinrichs AS, De Maio N, Gozashti L, Lanfear R, Haussler D and
Corbett-Detig R
4086:
4012:
3618:
1110:
Randomized
Axelerated Maximum Likelihood for High Performance Computing (nucleotides and aminoacids)
1346:
1307:
732:
for use with
Maximum Parsimony (via the CIPRES portal), Maximum Likelihood, and Bayesian analysis)
210:
109:
97:
3017:"RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference"
2468:"MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences"
2211:"IQ-Tree: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies"
987:
Explore, manipulate, analyze, and simulate phylogenetic objects (alignments, trees, and MCMC logs)
3966:
3764:
630:
also be used to build timetrees incorporating a geological timescale, with some optional modules.
3682:
532:
An efficient phylogenomic software by maximum likelihood, as successor of IQPNNI and Tree-Puzzle
4179:
4125:
3849:
3722:
3519:"T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks"
4101:
3779:
3478:"Tree-Puzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing"
3938:
3844:
2924:
2681:
2626:
2412:
2163:
1882:
1671:
51:(also simply referred to as parsimony), unweighted pair group method with arithmetic mean (
32:
2913:"ProtASR2: Ancestral reconstruction of protein sequences accounting for folding stability"
956:
Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors
8:
3981:
3863:
1945:
1286:
2928:
2685:
2630:
2416:
2167:
1954:
1886:
1675:
1517:"Reconstruction of clonal trees and tumor composition from multi-sample sequencing data"
460:
Fast phylogenetic inference for alignments with up to hundreds of thousands of sequences
3904:
3858:
3774:
3703:
3594:
3567:
3543:
3518:
3417:
3409:
3276:
3219:
3194:
3073:
3041:
3016:
2992:
2888:
2863:
2749:
2724:
2705:
2649:
2616:
2604:
2603:
Hellmuth M, Wieseke N, Lechner M, Lenhof HP, Middendorf M, Stadler PF (February 2015).
2536:
2443:
2400:
2376:
2349:
2330:
2284:
2259:
2235:
2210:
2186:
2149:
2093:
2014:
1967:
1905:
1870:
1846:
1821:
1694:
1657:
1592:
1565:
1541:
1516:
1492:
1467:
1311:
748:
60:
3494:
3477:
3453:
3436:
3368:
3341:
3135:
3110:
2572:
2555:
2466:
Haschka, Thomas; Ponger, Loic; Escudé, Christophe; Mozziconacci, Julien (2021-06-08).
119:
An algorithm for clonal tree reconstruction from multi-sample cancer sequencing data.
3832:
3648:
3640:
3635:
3599:
3548:
3499:
3458:
3392:
3373:
3322:
3281:
3263:
3224:
3175:
3140:
3091:
3087:
3046:
2997:
2979:
2975:
2940:
2893:
2844:
2795:
2754:
2697:
2654:
2585:
2577:
2528:
2523:
2506:
2487:
2483:
2448:
2430:
2381:
2334:
2289:
2240:
2191:
2130:
2055:
2006:
1998:
1971:
1959:
1910:
1851:
1740:
1699:
1638:
1597:
1546:
1497:
1340:
652:
140:
Patrick Kück, Sandra A Meid, Christian Groß, Bernhard Misof, Johann Wolfgang Wägele.
48:
28:
3437:"T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks"
3259:
3032:
2879:
2790:
2773:
2740:
2709:
2540:
2018:
1735:
1718:
1633:
1616:
1532:
808:
Computation of gene and species trees based on event-relations (orthology, paralogy)
729:
Web application to organize trait data (morphological characters) for tree building
557:
296:, B. Larget, D.A. Baum, S.D. Smith, A. Rokas and B. Larget, S.K. Kotha, C.N. Dewey,
3921:
3875:
3693:
3630:
3589:
3579:
3538:
3530:
3489:
3448:
3384:
3363:
3353:
3342:"Treefinder: a powerful graphical analysis environment for molecular phylogenetics"
3312:
3271:
3255:
3214:
3206:
3167:
3130:
3122:
3083:
3036:
3028:
2987:
2971:
2932:
2883:
2875:
2834:
2826:
2785:
2744:
2736:
2689:
2644:
2634:
2567:
2518:
2479:
2438:
2420:
2371:
2366:
2361:
2320:
2279:
2271:
2230:
2222:
2181:
2171:
2122:
2045:
1990:
1949:
1941:
1900:
1890:
1841:
1833:
1771:
1730:
1689:
1679:
1628:
1587:
1577:
1536:
1528:
1487:
1479:
1353:
1197:
Simulation of genetic data under diverse spatially explicit evolutionary scenarios
1026:
Simulation of protein sequences under structurally constrained substitution models
499:
44:
3126:
4022:
2959:
2467:
2425:
2401:"MicrobeTrace: Retooling molecular epidemiology for rapid public health response"
2176:
1994:
1684:
1164:
918:
326:
Chaos Game Representation (CGR) method, based on concepts of statistical physics
297:
293:
3243:
1483:
323:
CGR method for accurate classification and tracking of rapidly evolving viruses
100:
software package that contains the qpGraph, qpAdm, qpWave, and qpDstat programs
3996:
3617:
Piñeiro, César; Abuín, José M; Pichel, Juan C (2020-11-01). Ponty, Yann (ed.).
3584:
2609:
Proceedings of the National Academy of Sciences of the United States of America
2034:"Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks"
1875:
Proceedings of the National Academy of Sciences of the United States of America
1012:
Ancestral reconstruction of protein sequences accounting for folding stability
636:
40:
3709:
3388:
2839:
1929:
663:
507:
Maximum likelihood, neighbor-joining, clustering techniques, distance matrices
165:
Workflow platform dedicated to phylogenetic and general bioinformatic analysis
4153:
3991:
3961:
3868:
3745:
3644:
3267:
3171:
2983:
2944:
2848:
2701:
2581:
2491:
2434:
2002:
1806:
1582:
1216:
Computation, visualization and exploration of phylogenetic trees and networks
318:
3317:
3300:
3210:
2936:
2830:
2693:
2639:
2275:
2226:
2050:
2033:
1895:
1837:
1776:
1759:
1394:
276:
Distance and maximum likelihood methods (through PhyML, PHYLIP, Tree-Puzzle)
4096:
4042:
4037:
4032:
4017:
3825:
3820:
3652:
3603:
3552:
3503:
3462:
3396:
3377:
3358:
3326:
3285:
3228:
3095:
3050:
3001:
2897:
2799:
2758:
2658:
2589:
2532:
2452:
2385:
2293:
2244:
2195:
2134:
2126:
2059:
2010:
1963:
1914:
1855:
1744:
1703:
1642:
1601:
1550:
1501:
382:
Coestimation of substitution, recombination and dN/dS in protein sequences
3406:. If this is an intentional citation to a retracted paper, please replace
3179:
3144:
1764:
Journal of the Royal Statistical Society, Series A (Statistics in Society)
1230:
Parsimony, weighting, ratchet, tree drift, tree fusing, sectorial searches
1054:
Coestimation of recombination and substitution rates in protein sequences
4091:
3784:
3534:
2325:
2308:
2150:"FastTree 2--approximately maximum-likelihood trees for large alignments"
1324:
962:
A. G. Deshwar, S. Vembu, C. K. Yung, G. H. Jang, L. Stein, and Q. Morris
798:
409:
393:
290:
Bayesian concordance using modified greedy consensus of unrooted quartets
254:
2814:
538:
Lam-Tung Nguyen, O. Chernomor, H.A. Schmidt, A. von Haeseler, B.Q. Minh
3769:
1300:
1275:
1208:
928:
Generates phylogenetic trees in various formats, based on NCBI taxonomy
691:
Thomas Haschka, Loïc Ponger, Christophe Escudé and Julien Mozziconacci
371:
Simulation of multiple sequence alignments of DNA or protein sequences
92:
36:
1719:"BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny"
216:
Bayesian inference, multiple models, mixture model (auto-partitioning)
4106:
4070:
4065:
4060:
3955:
3837:
3675:
401:
Rooted trees, tanglegrams, consensus networks, hybridization networks
148:
970:
Fast and accurate estimation of phylogenies using maximum likelihood
3078:
2621:
2154:
2098:
2075:
Advances in Neural Information Processing Systems 31 (NeurIPS 2018)
1662:
176:
3475:
3015:
Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A (May 2019).
1514:
1200:
Coalescent, molecular evolution, DNA sequences, SNPs, STRs, RFLPs
2115:
International Journal of Systematic and Evolutionary Microbiology
740:
565:
398:
Tool for visualizing rooted trees and calculating rooted networks
348:
3714:
3476:
Schmidt HA, Strimmer K, Vingron M, von Haeseler A (March 2002).
1367:
Phylogenetic placement using maximum parsimony for viral genomes
246:
Bayesian inference, relaxed molecular clock, demographic history
3797:
3565:
2465:
2209:
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ (January 2015).
2088:
Ray S, Jia B, Safavi S, Opijnen T, Isberg R, Rosch J, Bento J.
1515:
El-Kebir M, Oesper L, Acheson-Field H, Raphael BJ (June 2015).
1432:
Rate estimation, branch length estimation, alignment annotation
907:
680:
3301:"Application of phylogenetic networks in evolutionary studies"
3241:
2812:
3926:
3854:
3108:
2208:
1424:
1378:
1153:
Simulation of genome-wide evolution along phylogenetic trees
847:
52:
2602:
1617:"APE: Analyses of Phylogenetics and Evolution in R language"
598:
Distance, Parsimony and Maximum Composite Likelihood Methods
310:
Maximum Likelihood, Markov Chain Monte Carlo (MCMC) methods
171:
E. Lord, M. Leclercq, A. Boc, A.B. Diallo and V. Makarenkov
1656:
Lord E, Leclercq M, Boc A, Diallo AB, Makarenkov V (2012).
1564:
Kück P, Meid SA, Groß C, Wägele JW, Misof B (August 2014).
1465:
3157:
1793:
BayesPhylogenies 1.0. Software distributed by the authors.
1130:
A. Kozlov, D. Darriba, T. Flouri, B. Morel, A. Stamatakis
1043:
Simulating sequences forward in time, substitution models
852:
Phylogenetic analysis using parsimony (*and other methods)
724:
238:
198:
Bayesian inference, demographic history, population splits
181:
Simultaneous Bayesian inference of alignment and phylogeny
16:
Compilation of software used to produce phylogenetic trees
1819:
3339:
3195:"Automation and Evaluation of the SOWH Test with SOWHAT"
3014:
2398:
885:
phylogenetics functions, STAR, NJst, STEAC, maxtree, etc
195:
Bayesian Analysis of Trees With Internal Node Generation
125:
M. El-Kebir, L. Oesper, H. Acheson-Field, B. J. Raphael
668:
MicrobeTrace is a free, browser-based web application.
340:
Exhaustive search, Quadratic Integer Programming (QIP)
3685:
of phylogenetic tools (reconstruction, visualization,
2257:
1822:"Bayesian phylogenetics with BEAUti and the BEAST 1.7"
915:
Maximum parsimony, distance matrix, maximum likelihood
855:
Maximum parsimony, distance matrix, maximum likelihood
633:
Maximum parsimony, distance matrix, maximum likelihood
579:
Three-item analysis for phylogenetics and biogeography
249:
A. J. Drummond, M. A. Suchard, D Xie & A. Rambaut
2671:
1984:
1655:
1614:
1142:
A hybrid maximum-likelihood – neighbor-joining method
648:
selection of best substitution model and parameters.
343:
S. Malikic, A.W. McPherson, N. Donmez, C.S. Sahinalp
122:
Maximum Likelihood, Integer Linear Programming (ILP)
3793:
3063:
2260:"Ultrafast approximation for phylogenetic bootstrap"
1869:
Jiang Y, Qiu Y, Minn AJ, Zhang NR (September 2016).
942:
Quartet implementation (uses sequences or distances)
488:
Geneious provides genome and proteome research tools
184:
Bayesian inference, alignment as well as tree search
3516:
2556:"MRBAYES: Bayesian inference of phylogenetic trees"
2553:
2505:O'Leary, Maureen A.; Kaufman, Seth (October 2011).
1292:
Maximum likelihood, maximum parsimony, and distance
1046:M. Arenas, H.G. Dos Santos, D. Posada, U. Bastolla
154:
Provides a large variety of phylogenetics functions
151:
package for analysis of phylogenetics and evolution
3616:
2504:
1757:
1563:
839:R, two‐stage Bayesian inference using MrBayes 3.2
2774:"Phybase: an R package for species tree analysis"
2090:Exact inference under the perfect phylogeny model
2072:
1868:
1820:Drummond A, Suchard MA, Xie D, Rambaut A (2012).
1807:"BayesTraits. Computer program and documentation"
1255:Tree construction given precomputed distance data
735:O'Leary, M. A., and S. Kaufman, also K. Alphonse
4151:
3340:Jobb G, von Haeseler A, Strimmer K (June 2004).
2861:
2554:Huelsenbeck, J. P.; Ronquist, F. (August 2001).
2031:
1928:Thind, Amarinder Singh; Sinha, Somdatta (2023).
1716:
1615:Paradis E, Claude J, Strimmer K (January 2004).
1448:List of phylogenetic tree visualization software
1405:César Piñeiro. José M. Abuín and Juan C. Pichel
616:Maximum Likelihood (RAxML) and Neighbor-Joining
388:M. Arenas, J.S. Lopes, M.A. Beaumont, D. Posada
2258:Minh BQ, Nguyen MA, von Haeseler A (May 2013).
2147:
2087:
767:Median Joining, Reduced Median, Steiner Network
713:Molecular phylogenetics (protein or nucleotide)
446:Optimized maximum likelihood (nucleotides only)
3192:
2910:
2112:
1156:Simulating genome-wide sequences forward time
1074:D. Darriba, GL. Taboada, R. Doallo, D. Posada
552:D. Darriba, GL. Taboada, R. Doallo, D. Posada
510:S.L. Kosakovsky Pond, S.D.W. Frost, S.V. Muse
337:Clonality Inference in Tumors Using Phylogeny
313:Y. Jiang, Y. Qiu, A. J. Minn, and N. R. Zhang
3730:
3193:Church SH, Ryan JF, Dunn CW (November 2015).
2596:
1758:Wilson IJ, Weale ME, Balding DJ (June 2003).
1459:
781:Maximum parsimony, implied weighting, ratchet
585:J. Ducasse, N. Cao & R. Zaragüeta-Bagils
243:Bayesian Evolutionary Analysis Sampling Trees
43:. Methods for estimating phylogenies include
3559:
3517:Boc A, Diallo AB, Makarenkov V (July 2012).
3510:
3469:
3428:
3333:
3186:
2106:
2025:
1813:
1145:M. Ninio, E. Privman, T. Pupko, N. Friedman
1127:Maximum likelihood, simple Maximum parsimony
1113:Maximum likelihood, simple Maximum parsimony
549:Maximum likelihood, AIC, BIC, DT, hLTR, dLTR
3710:https://github.com/CDCgov/MicrobeTrace/wiki
3298:
2862:Brown JW, Walker JF, Smith SA (June 2017).
2507:"MorphoBank: phylophenomics in the "cloud""
2148:Price MN, Dehal PS, Arkin AP (March 2010).
1710:
1649:
1608:
1557:
1329:Maximum likelihood and statistical analysis
1032:M. Arenas, A. Sanchez-Cobos, U. Bastolla U
1004:A. Varon, N. Lucaroni, L. Hong, W. Wheeler
792:Phylogenetic analysis by maximum likelihood
658:Michel C. Milinkovitch and Raphaël Helaers
651:Maximum likelihood, stochastic heuristics (
494:A. J. Drummond, M.Suchard, V.Lefort et al.
3737:
3723:
3434:
3420:|...|intentional=yes}}
1927:
1804:
1790:
1096:Tree construction optimized for efficiency
1029:Simulating sequences, substitution models
984:Unix/Linux command line phylogenetic tools
899:Maximum likelihood of Finite Mixture Modes
518:Iterative ML treesearch with stopping rule
3634:
3593:
3583:
3542:
3493:
3452:
3367:
3357:
3316:
3275:
3218:
3134:
3077:
3040:
2991:
2887:
2838:
2789:
2748:
2648:
2638:
2620:
2571:
2522:
2442:
2424:
2375:
2365:
2347:
2324:
2306:
2283:
2234:
2185:
2175:
2097:
2049:
2032:Huson DH, Scornavacca C (December 2012).
1953:
1904:
1894:
1845:
1775:
1734:
1693:
1683:
1632:
1591:
1581:
1540:
1491:
1386:GUI with PHYLIP 3.6 and IQTree algorithms
1316:Maximum likelihood, distances, and others
1272:Distance matrix and approximate parsimony
896:Phylogenetic Clustering (Phyloclustering)
828:R. Lanfear, B Calcott, SYW Ho, S Guindon
795:Maximum likelihood and Bayesian inference
418:Brute force search and homotopy algorithm
1717:Suchard MA, Redelings BD (August 2006).
1015:Maximum likelihood, substitution models
990:J.W. Brown, J.F. Walker, and S.A. Smith
601:Tamura K, Dudley J, Nei M & Kumar S
595:Molecular Evolutionary Genetics Analysis
2722:
1383:Fast and free multiplatform tree editor
1285:Tree construction algorithm within the
699:Model selection (protein or nucleotide)
354:Progressive multiple sequence alignment
4152:
3694:list of evolutionary genetics software
2957:
2911:Arenas, Miguel; Bastolla, Ugo (2020).
2725:"phangorn: phylogenetic analysis in R"
1349:detection, multiple sequence alignment
882:an R package for species tree analysis
524:L.S. Vinh, A. von Haeseler, B.Q. Minh
329:Amarinder Singh Thind, Somdatta Sinha
3718:
2771:
4132:
3704:Zoological Research Museum A. Koenig
3299:Huson DH, Bryant D (February 2006).
3160:AIDS Research and Human Retroviruses
1946:10.2174/0113892029264990231013112156
1468:"Ancient admixture in human history"
1082:Software library for genomic biology
836:R package for phylogenetic assembly
811:Cograph-Editing and Triple-Inference
521:Maximum likelihood, neighbor-joining
504:Hypothesis testing using phylogenies
421:Jia B., Ray S., Safavi S., Bento J.
2864:"Phyx: phylogenetic tools for unix"
1987:Current Protocols in Bioinformatics
1413:GUI and tree editor (requires Nona)
1319:Jobb G, von Haeseler A, Strimmer K
1247:Iain Milne, Dominik Lindner et al.
466:M.N. Price, P.S. Dehal, A.P. Arkin
13:
1345:Tree inference and visualization,
1175:S. Samson, E. Lord, V. Makarenkov
825:Maximum likelihood, AIC, AICc, BIC
764:Free Phylogenetic Network Software
287:Bayesian concordance of gene trees
209:Bayesian inference of trees using
31:. Such tools are commonly used in
14:
4191:
3744:
3662:
1057:Approximate Bayesian computation
385:Approximate Bayesian computation
4175:Lists of bioinformatics software
4131:
4120:
4119:
3972:Phylogenetic comparative methods
3796:
2917:Methods in Ecology and Evolution
2674:Methods in Ecology and Evolution
2524:10.1111/j.1096-0031.2011.00355.x
1071:Maximum likelihood, AIC, BIC, DT
745:Posterior probability estimation
357:Distance matrix/nearest neighbor
3977:Phylogenetic niche conservatism
3610:
3495:10.1093/bioinformatics/18.3.502
3454:10.1093/bioinformatics/17.7.664
3305:Molecular Biology and Evolution
3292:
3235:
3151:
3102:
3057:
3008:
2951:
2904:
2855:
2806:
2765:
2716:
2665:
2573:10.1093/bioinformatics/17.8.754
2547:
2498:
2459:
2392:
2341:
2300:
2264:Molecular Biology and Evolution
2251:
2215:Molecular Biology and Evolution
2202:
2141:
2081:
2066:
1978:
1921:
1862:
1826:Molecular Biology and Evolution
1402:Approximate maximum likelihood
1359:Boc A, Diallo AB, Makarenkov V
1102:K. Howe, A. Bateman, R. Durbin
265:L. Vauterin & P. Vauterin.
201:I. J. Wilson, Weale, D.Balding
57:Bayesian phylogenetic inference
3678:List of phylogenetics programs
3636:10.1093/bioinformatics/btaa582
3088:10.1093/bioinformatics/btac287
2976:10.1093/bioinformatics/btab617
2484:10.1093/bioinformatics/btab430
2367:10.12688/f1000research.26930.1
1798:
1784:
1751:
1627:(2). Oxford, England: 289–90.
1508:
463:Approximate maximum likelihood
187:M.A. Suchard, B. D. Redelings
21:list of phylogenetics software
1:
3260:10.1093/bioinformatics/btz311
3127:10.1128/JVI.73.1.152-160.1999
3033:10.1093/bioinformatics/btz305
2958:Arenas, Miguel (2021-08-27).
2880:10.1093/bioinformatics/btx063
2791:10.1093/bioinformatics/btq062
2741:10.1093/bioinformatics/btq706
2605:"Phylogenomics with paralogs"
2348:Criscuolo A (November 2020).
1736:10.1093/bioinformatics/btl175
1634:10.1093/bioinformatics/btg412
1533:10.1093/bioinformatics/btv261
1453:
157:Maintainer: Emmanuel Paradis
3529:(Web Server issue): W573–9.
2723:Schliep KP (February 2011).
2426:10.1371/journal.pcbi.1009300
2177:10.1371/journal.pone.0009490
1995:10.1002/0471250953.bi0203s00
1685:10.1371/journal.pone.0029903
976:S. Guindon & O. Gascuel
162:Armadillo Workflow Platform
7:
3897:Phylogenetic reconciliation
3804:Evolutionary biology portal
3760:Computational phylogenetics
2313:Research Ideas and Outcomes
1989:. Chapter 2: 2.3.1–2.3.22.
1484:10.1534/genetics.112.145037
1441:
912:PHYLogeny Inference Package
25:computational phylogenetics
10:
4196:
3708:MicrobeTrace available at
3585:10.1038/s41588-021-00862-7
3435:Makarenkov V (July 2001).
2772:Liu L, Yu L (April 2010).
2405:PLOS Computational Biology
1416:Maximum parsimony, ratchet
866:Phylogenetic analysis in R
719:J. Adachi and M. Hasegawa
279:S. Ramirez, E. Rodriguez.
4115:
4087:Phylogenetic nomenclature
4079:
4053:
4005:
3947:
3884:
3813:
3791:
3752:
3389:10.1186/s12862-015-0513-z
2307:Criscuolo A (June 2019).
1805:Pagel M, Meade A (2007).
1791:Pagel M, Meade A (2007),
1219:D.H. Huson and D. Bryant
27:software used to produce
3346:BMC Evolutionary Biology
3172:10.1089/aid.1995.11.1423
1583:10.1186/1471-2105-15-294
1347:Horizontal gene transfer
1213:Tree and network program
609:MegAlign Pro is part of
211:Markov chain Monte Carlo
3967:Molecular phylogenetics
3917:Distance-matrix methods
3765:Molecular phylogenetics
2937:10.1111/2041-210X.13341
2694:10.1111/2041-210X.12117
2640:10.1073/pnas.1412770112
1896:10.1073/pnas.1522203113
1777:10.1111/1467-985X.00264
1269:Efficient hybrid method
1018:M. Arenas, U. Bastolla
872:Maintainer: K. Schliep
70:
65:distance matrix methods
4170:Genetics-related lists
4160:Phylogenetics software
3987:Phylogenetics software
3901:Probabilistic methods
3850:Long branch attraction
3523:Nucleic Acids Research
3359:10.1186/1471-2148-4-18
2127:10.1099/ijs.0.059360-0
1241:Phylogenetic inference
1227:Phylogenetic inference
778:Phylogenetic inference
3780:Evolutionary taxonomy
3700:phylogenetic software
3412:|...}}
3383:(Retracted, see
3318:10.1093/molbev/msj030
3211:10.1093/sysbio/syv055
2831:10.1093/sysbio/syq010
2276:10.1093/molbev/mst024
2227:10.1093/molbev/msu300
2077:. pp. 4108–4118.
2051:10.1093/sysbio/sys062
1838:10.1093/molbev/mss075
1159:Arenas M., Posada D.
374:M. Arenas, D. Posada
3939:Three-taxon analysis
3845:Phylogenetic network
3672:phylogeny webservers
2326:10.3897/rio.5.e36178
1429:Phylo-grammar engine
404:Daniel Huson et al.
33:comparative genomics
23:is a compilation of
3982:Phylogenetic signal
3115:Journal of Virology
2929:2020MEcEv..11..248A
2686:2013MEcEv...4.1011T
2631:2015PNAS..112.2058H
2417:2021PLSCB..17E9300C
2168:2010PLoSO...5.9490P
1887:2016PNAS..113E5528J
1809:. pp. 1216–23.
1676:2012PLoSO...729903L
1233:P. Goloboff et al.
1189:Church, Ryan, Dunn
888:L. Liu & L. Yu
842:Thomas et al. 2013
639:and D. R. Maddison
582:Three-item analysis
233:M. Pagel, A. Meade
219:M. Pagel, A. Meade
4165:Genetics databases
3910:Bayesian inference
3905:Maximum likelihood
3683:comprehensive list
3535:10.1093/nar/gks485
3199:Systematic Biology
2840:20.500.11850/25281
2819:Systematic Biology
2038:Systematic Biology
1570:BMC Bioinformatics
1332:Maximum likelihood
1312:scripting language
1183:Hypothesis testing
1051:ProteinEvolverABC
973:Maximum likelihood
749:Bayesian inference
716:Maximum likelihood
702:Maximum likelihood
477:Maximum likelihood
449:Maximum likelihood
61:maximum likelihood
29:phylogenetic trees
4147:
4146:
3892:Maximum parsimony
3885:Inference methods
3833:Phylogenetic tree
3668:Complete list of
3629:(17): 4658–4659.
3254:(21): 4480–4483.
3166:(11): 1423–1425.
3072:(11): 3118–3120.
3027:(21): 4453–4455.
2874:(12): 1886–1888.
2680:(11): 1011–1017.
2478:(21): 3947–3949.
1439:
1438:
1370:Maximum parsimony
1341:T-REX (Webserver)
1203:M. Currat et al.
653:genetic algorithm
206:BayesPhylogenies
49:maximum parsimony
4187:
4135:
4134:
4123:
4122:
3922:Neighbor-joining
3876:Ghost population
3806:
3801:
3800:
3739:
3732:
3725:
3716:
3715:
3702:provided by the
3670:Institut Pasteur
3657:
3656:
3638:
3614:
3608:
3607:
3597:
3587:
3563:
3557:
3556:
3546:
3514:
3508:
3507:
3497:
3473:
3467:
3466:
3456:
3432:
3426:
3425:
3423:
3421:
3413:
3402:Retraction Watch
3381:
3371:
3361:
3337:
3331:
3330:
3320:
3296:
3290:
3289:
3279:
3239:
3233:
3232:
3222:
3190:
3184:
3183:
3155:
3149:
3148:
3138:
3106:
3100:
3099:
3081:
3061:
3055:
3054:
3044:
3012:
3006:
3005:
2995:
2955:
2949:
2948:
2908:
2902:
2901:
2891:
2859:
2853:
2852:
2842:
2810:
2804:
2803:
2793:
2769:
2763:
2762:
2752:
2720:
2714:
2713:
2669:
2663:
2662:
2652:
2642:
2624:
2600:
2594:
2593:
2575:
2551:
2545:
2544:
2526:
2502:
2496:
2495:
2463:
2457:
2456:
2446:
2428:
2396:
2390:
2389:
2379:
2369:
2345:
2339:
2338:
2328:
2304:
2298:
2297:
2287:
2255:
2249:
2248:
2238:
2206:
2200:
2199:
2189:
2179:
2145:
2139:
2138:
2121:(Pt 2): 689–91.
2110:
2104:
2103:
2101:
2085:
2079:
2078:
2070:
2064:
2063:
2053:
2029:
2023:
2022:
1982:
1976:
1975:
1957:
1934:Current Genomics
1925:
1919:
1918:
1908:
1898:
1881:(37): E5528-37.
1866:
1860:
1859:
1849:
1832:(8): 1969–1973.
1817:
1811:
1810:
1802:
1796:
1795:
1788:
1782:
1781:
1779:
1755:
1749:
1748:
1738:
1714:
1708:
1707:
1697:
1687:
1653:
1647:
1646:
1636:
1612:
1606:
1605:
1595:
1585:
1561:
1555:
1554:
1544:
1512:
1506:
1505:
1495:
1463:
1354:neighbor joining
1099:Neighbor-joining
819:PartitionFinder
753:J. Huelsenbeck,
432:Neighbor Joining
360:Thompson et al.
75:
74:
45:neighbor-joining
4195:
4194:
4190:
4189:
4188:
4186:
4185:
4184:
4150:
4149:
4148:
4143:
4111:
4075:
4049:
4023:Symplesiomorphy
4001:
3943:
3880:
3809:
3802:
3795:
3789:
3753:Relevant fields
3748:
3743:
3665:
3660:
3615:
3611:
3572:Nature Genetics
3564:
3560:
3515:
3511:
3474:
3470:
3433:
3429:
3415:
3407:
3405:
3382:
3338:
3334:
3297:
3293:
3240:
3236:
3191:
3187:
3156:
3152:
3107:
3103:
3062:
3058:
3013:
3009:
2956:
2952:
2909:
2905:
2860:
2856:
2811:
2807:
2770:
2766:
2721:
2717:
2670:
2666:
2601:
2597:
2552:
2548:
2503:
2499:
2464:
2460:
2411:(9): e1009300.
2397:
2393:
2346:
2342:
2305:
2301:
2256:
2252:
2207:
2203:
2146:
2142:
2111:
2107:
2086:
2082:
2071:
2067:
2030:
2026:
1983:
1979:
1926:
1922:
1867:
1863:
1818:
1814:
1803:
1799:
1789:
1785:
1756:
1752:
1715:
1711:
1654:
1650:
1613:
1609:
1562:
1558:
1513:
1509:
1464:
1460:
1456:
1444:
1258:Distance matrix
1037:ProteinEvolver
696:Modelgenerator
681:MNHN-Tree-Tools
73:
17:
12:
11:
5:
4193:
4183:
4182:
4177:
4172:
4167:
4162:
4145:
4144:
4142:
4141:
4129:
4116:
4113:
4112:
4110:
4109:
4104:
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4094:
4089:
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4077:
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4074:
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4068:
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4057:
4055:
4051:
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4048:
4047:
4046:
4045:
4040:
4035:
4027:
4026:
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4020:
4009:
4007:
4003:
4002:
4000:
3999:
3997:Phylogeography
3994:
3989:
3984:
3979:
3974:
3969:
3964:
3959:
3951:
3949:
3948:Current topics
3945:
3944:
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3914:
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3879:
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3871:
3861:
3852:
3847:
3842:
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3830:
3829:
3828:
3817:
3815:
3814:Basic concepts
3811:
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3808:
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3690:
3679:
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3664:
3663:External links
3661:
3659:
3658:
3623:Bioinformatics
3609:
3578:(6): 809–816.
3558:
3509:
3482:Bioinformatics
3468:
3441:Bioinformatics
3427:
3332:
3291:
3248:Bioinformatics
3234:
3205:(6): 1048–58.
3185:
3150:
3121:(1): 152–160.
3101:
3066:Bioinformatics
3056:
3021:Bioinformatics
3007:
2964:Bioinformatics
2950:
2923:(2): 248–257.
2903:
2868:Bioinformatics
2854:
2825:(3): 307–321.
2805:
2778:Bioinformatics
2764:
2729:Bioinformatics
2715:
2664:
2615:(7): 2058–63.
2595:
2566:(8): 754–755.
2560:Bioinformatics
2546:
2517:(5): 529–537.
2497:
2472:Bioinformatics
2458:
2391:
2340:
2299:
2270:(5): 1188–95.
2250:
2201:
2140:
2105:
2080:
2065:
2024:
1977:
1940:(3): 187–195.
1920:
1861:
1812:
1797:
1783:
1750:
1729:(16): 2047–8.
1723:Bioinformatics
1709:
1648:
1621:Bioinformatics
1607:
1556:
1527:(12): i62-70.
1521:Bioinformatics
1507:
1478:(3): 1065–93.
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1088:Knight et al.
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945:Quartet method
943:
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922:
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919:J. Felsenstein
916:
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902:Wei-Chen Chen
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673:
669:
666:
660:
659:
656:
649:
645:
641:
640:
637:Wayne Maddison
634:
631:
627:
623:
622:
617:
614:
607:
603:
602:
599:
596:
593:
587:
586:
583:
580:
577:
573:
572:
569:
563:
560:
554:
553:
550:
547:
544:
540:
539:
536:
533:
530:
526:
525:
522:
519:
516:
512:
511:
508:
505:
502:
496:
495:
492:
489:
486:
482:
481:
478:
475:
472:
468:
467:
464:
461:
458:
454:
453:
450:
447:
444:
440:
439:
433:
430:
427:
423:
422:
419:
416:
412:
406:
405:
402:
399:
396:
390:
389:
386:
383:
380:
376:
375:
372:
369:
366:
362:
361:
358:
355:
352:
345:
344:
341:
338:
335:
331:
330:
327:
324:
321:
315:
314:
311:
308:
305:
301:
300:
291:
288:
285:
281:
280:
277:
274:
271:
267:
266:
263:
260:
257:
251:
250:
247:
244:
241:
235:
234:
231:
230:Trait analysis
228:
225:
221:
220:
217:
214:
207:
203:
202:
199:
196:
193:
189:
188:
185:
182:
179:
173:
172:
169:
166:
163:
159:
158:
155:
152:
146:
142:
141:
138:
134:
131:
127:
126:
123:
120:
117:
113:
112:
106:Nick Patterson
103:
101:
95:
89:
88:
85:
82:
79:
72:
69:
41:bioinformatics
15:
9:
6:
4:
3:
2:
4192:
4181:
4180:Phylogenetics
4178:
4176:
4173:
4171:
4168:
4166:
4163:
4161:
4158:
4157:
4155:
4140:
4139:
4130:
4128:
4127:
4118:
4117:
4114:
4108:
4105:
4103:
4100:
4098:
4095:
4093:
4090:
4088:
4085:
4084:
4082:
4078:
4072:
4069:
4067:
4064:
4062:
4059:
4058:
4056:
4052:
4044:
4041:
4039:
4036:
4034:
4031:
4030:
4028:
4024:
4021:
4019:
4016:
4015:
4014:
4011:
4010:
4008:
4004:
3998:
3995:
3993:
3992:Phylogenomics
3990:
3988:
3985:
3983:
3980:
3978:
3975:
3973:
3970:
3968:
3965:
3963:
3962:DNA barcoding
3960:
3958:
3957:
3953:
3952:
3950:
3946:
3940:
3937:
3933:
3932:Least squares
3930:
3928:
3925:
3923:
3920:
3919:
3918:
3915:
3911:
3908:
3906:
3903:
3902:
3900:
3898:
3895:
3893:
3890:
3889:
3887:
3883:
3877:
3874:
3870:
3869:Ghost lineage
3867:
3866:
3865:
3862:
3860:
3856:
3853:
3851:
3848:
3846:
3843:
3839:
3836:
3835:
3834:
3831:
3827:
3824:
3823:
3822:
3819:
3818:
3816:
3812:
3805:
3799:
3794:
3786:
3783:
3781:
3778:
3776:
3773:
3771:
3768:
3766:
3763:
3761:
3758:
3757:
3755:
3751:
3747:
3746:Phylogenetics
3740:
3735:
3733:
3728:
3726:
3721:
3720:
3717:
3711:
3707:
3705:
3701:
3697:
3695:
3691:
3688:
3684:
3680:
3677:
3674:
3671:
3667:
3666:
3654:
3650:
3646:
3642:
3637:
3632:
3628:
3624:
3620:
3613:
3605:
3601:
3596:
3591:
3586:
3581:
3577:
3573:
3569:
3562:
3554:
3550:
3545:
3540:
3536:
3532:
3528:
3524:
3520:
3513:
3505:
3501:
3496:
3491:
3487:
3483:
3479:
3472:
3464:
3460:
3455:
3450:
3446:
3442:
3438:
3431:
3419:
3411:
3404:
3403:
3398:
3394:
3390:
3386:
3379:
3375:
3370:
3365:
3360:
3355:
3351:
3347:
3343:
3336:
3328:
3324:
3319:
3314:
3311:(2): 254–67.
3310:
3306:
3302:
3295:
3287:
3283:
3278:
3273:
3269:
3265:
3261:
3257:
3253:
3249:
3245:
3238:
3230:
3226:
3221:
3216:
3212:
3208:
3204:
3200:
3196:
3189:
3181:
3177:
3173:
3169:
3165:
3161:
3154:
3146:
3142:
3137:
3132:
3128:
3124:
3120:
3116:
3112:
3105:
3097:
3093:
3089:
3085:
3080:
3075:
3071:
3067:
3060:
3052:
3048:
3043:
3038:
3034:
3030:
3026:
3022:
3018:
3011:
3003:
2999:
2994:
2989:
2985:
2981:
2977:
2973:
2969:
2965:
2961:
2954:
2946:
2942:
2938:
2934:
2930:
2926:
2922:
2918:
2914:
2907:
2899:
2895:
2890:
2885:
2881:
2877:
2873:
2869:
2865:
2858:
2850:
2846:
2841:
2836:
2832:
2828:
2824:
2820:
2816:
2809:
2801:
2797:
2792:
2787:
2783:
2779:
2775:
2768:
2760:
2756:
2751:
2746:
2742:
2738:
2734:
2730:
2726:
2719:
2711:
2707:
2703:
2699:
2695:
2691:
2687:
2683:
2679:
2675:
2668:
2660:
2656:
2651:
2646:
2641:
2636:
2632:
2628:
2623:
2618:
2614:
2610:
2606:
2599:
2591:
2587:
2583:
2579:
2574:
2569:
2565:
2561:
2557:
2550:
2542:
2538:
2534:
2530:
2525:
2520:
2516:
2512:
2508:
2501:
2493:
2489:
2485:
2481:
2477:
2473:
2469:
2462:
2454:
2450:
2445:
2440:
2436:
2432:
2427:
2422:
2418:
2414:
2410:
2406:
2402:
2395:
2387:
2383:
2378:
2373:
2368:
2363:
2359:
2355:
2354:F1000Research
2351:
2344:
2336:
2332:
2327:
2322:
2318:
2314:
2310:
2303:
2295:
2291:
2286:
2281:
2277:
2273:
2269:
2265:
2261:
2254:
2246:
2242:
2237:
2232:
2228:
2224:
2221:(1): 268–74.
2220:
2216:
2212:
2205:
2197:
2193:
2188:
2183:
2178:
2173:
2169:
2165:
2161:
2157:
2156:
2151:
2144:
2136:
2132:
2128:
2124:
2120:
2116:
2109:
2100:
2095:
2091:
2084:
2076:
2069:
2061:
2057:
2052:
2047:
2044:(6): 1061–7.
2043:
2039:
2035:
2028:
2020:
2016:
2012:
2008:
2004:
2000:
1996:
1992:
1988:
1981:
1973:
1969:
1965:
1961:
1956:
1951:
1947:
1943:
1939:
1935:
1931:
1924:
1916:
1912:
1907:
1902:
1897:
1892:
1888:
1884:
1880:
1876:
1872:
1865:
1857:
1853:
1848:
1843:
1839:
1835:
1831:
1827:
1823:
1816:
1808:
1801:
1794:
1787:
1778:
1773:
1770:(2): 155–88.
1769:
1765:
1761:
1754:
1746:
1742:
1737:
1732:
1728:
1724:
1720:
1713:
1705:
1701:
1696:
1691:
1686:
1681:
1677:
1673:
1670:(1): e29903.
1669:
1665:
1664:
1659:
1652:
1644:
1640:
1635:
1630:
1626:
1622:
1618:
1611:
1603:
1599:
1594:
1589:
1584:
1579:
1575:
1571:
1567:
1560:
1552:
1548:
1543:
1538:
1534:
1530:
1526:
1522:
1518:
1511:
1503:
1499:
1494:
1489:
1485:
1481:
1477:
1473:
1469:
1462:
1458:
1449:
1446:
1445:
1434:
1431:
1428:
1426:
1423:
1422:
1418:
1415:
1412:
1409:
1408:
1404:
1401:
1398:
1396:
1393:
1392:
1388:
1385:
1382:
1380:
1377:
1376:
1372:
1369:
1366:
1363:
1362:
1358:
1355:
1351:
1348:
1344:
1342:
1339:
1338:
1334:
1331:
1328:
1326:
1323:
1322:
1318:
1315:
1313:
1309:
1304:
1302:
1299:
1298:
1294:
1291:
1289:package for R
1288:
1284:
1281:
1280:
1277:
1274:
1271:
1268:
1265:
1264:
1260:
1257:
1254:
1251:
1250:
1246:
1243:
1240:
1237:
1236:
1232:
1229:
1226:
1223:
1222:
1218:
1215:
1212:
1210:
1207:
1206:
1202:
1199:
1196:
1193:
1192:
1188:
1185:
1182:
1179:
1178:
1174:
1171:
1168:
1166:
1163:
1162:
1158:
1155:
1152:
1149:
1148:
1144:
1141:
1137:
1134:
1133:
1129:
1126:
1123:
1120:
1119:
1115:
1112:
1109:
1106:
1105:
1101:
1098:
1095:
1092:
1091:
1087:
1084:
1081:
1078:
1077:
1073:
1070:
1067:
1064:
1063:
1059:
1056:
1053:
1050:
1049:
1045:
1042:
1039:
1036:
1035:
1031:
1028:
1025:
1022:
1021:
1017:
1014:
1011:
1008:
1007:
1003:
1000:
997:
994:
993:
989:
986:
983:
980:
979:
975:
972:
969:
966:
965:
961:
958:
955:
952:
951:
947:
944:
941:
938:
937:
933:
930:
927:
924:
923:
920:
917:
914:
911:
909:
906:
905:
901:
898:
895:
892:
891:
887:
884:
881:
879:
876:
875:
871:
868:
865:
862:
861:
857:
854:
851:
849:
846:
845:
841:
838:
835:
832:
831:
827:
824:
821:
818:
817:
813:
810:
807:
804:
803:
800:
797:
794:
791:
788:
787:
783:
780:
777:
774:
773:
769:
766:
763:
760:
759:
756:
752:
750:
747:
744:
742:
739:
738:
734:
731:
728:
726:
723:
722:
718:
715:
712:
709:
708:
705:Thomas Keane
704:
701:
698:
695:
694:
690:
687:
684:
682:
679:
678:
674:
670:
667:
665:
662:
661:
657:
654:
650:
646:
643:
642:
638:
635:
632:
628:
625:
624:
621:
618:
615:
612:
608:
606:MegAlign Pro
605:
604:
600:
597:
594:
592:
589:
588:
584:
581:
578:
575:
574:
571:A. Criscuolo
570:
567:
564:
561:
559:
556:
555:
551:
548:
545:
543:jModelTest 2
542:
541:
537:
534:
531:
528:
527:
523:
520:
517:
514:
513:
509:
506:
503:
501:
498:
497:
493:
490:
487:
484:
483:
479:
476:
473:
470:
469:
465:
462:
459:
456:
455:
451:
448:
445:
442:
441:
438:
434:
431:
428:
425:
424:
420:
417:
413:
411:
408:
407:
403:
400:
397:
395:
392:
391:
387:
384:
381:
378:
377:
373:
370:
367:
364:
363:
359:
356:
353:
350:
347:
346:
342:
339:
336:
333:
332:
328:
325:
322:
320:
317:
316:
312:
309:
306:
303:
302:
299:
295:
292:
289:
286:
283:
282:
278:
275:
272:
269:
268:
264:
261:
258:
256:
253:
252:
248:
245:
242:
240:
237:
236:
232:
229:
226:
223:
222:
218:
215:
212:
208:
205:
204:
200:
197:
194:
191:
190:
186:
183:
180:
178:
175:
174:
170:
167:
164:
161:
160:
156:
153:
150:
147:
144:
143:
139:
135:
132:
129:
128:
124:
121:
118:
115:
114:
111:
107:
104:
102:
99:
96:
94:
91:
90:
86:
83:
80:
77:
76:
68:
66:
62:
58:
54:
50:
46:
42:
38:
34:
30:
26:
22:
4136:
4124:
4097:Sister group
4080:Nomenclature
4043:Autapomorphy
4038:Synapomorphy
4018:Plesiomorphy
4006:Group traits
3986:
3954:
3826:Cladogenesis
3821:Phylogenesis
3686:
3626:
3622:
3612:
3575:
3571:
3561:
3526:
3522:
3512:
3488:(3): 502–4.
3485:
3481:
3471:
3447:(7): 664–8.
3444:
3440:
3430:
3416:{{
3408:{{
3401:
3399:,
3349:
3345:
3335:
3308:
3304:
3294:
3251:
3247:
3237:
3202:
3198:
3188:
3163:
3159:
3153:
3118:
3114:
3104:
3069:
3065:
3059:
3024:
3020:
3010:
2970:(1): 58–64.
2967:
2963:
2953:
2920:
2916:
2906:
2871:
2867:
2857:
2822:
2818:
2808:
2784:(7): 962–3.
2781:
2777:
2767:
2735:(4): 592–3.
2732:
2728:
2718:
2677:
2673:
2667:
2612:
2608:
2598:
2563:
2559:
2549:
2514:
2510:
2500:
2475:
2471:
2461:
2408:
2404:
2394:
2357:
2353:
2343:
2316:
2312:
2302:
2267:
2263:
2253:
2218:
2214:
2204:
2162:(3): e9490.
2159:
2153:
2143:
2118:
2114:
2108:
2089:
2083:
2074:
2068:
2041:
2037:
2027:
1986:
1980:
1937:
1933:
1923:
1878:
1874:
1864:
1829:
1825:
1815:
1800:
1792:
1786:
1767:
1763:
1753:
1726:
1722:
1712:
1667:
1661:
1651:
1624:
1620:
1610:
1573:
1569:
1559:
1524:
1520:
1510:
1475:
1471:
1461:
1395:VeryFastTree
858:D. Swofford
784:P. Goloboff
754:
664:MicrobeTrace
436:
224:BayesTraits
20:
18:
4092:Crown group
4054:Group types
3785:Systematics
1335:Makarenkov
1325:Tree-Puzzle
1261:ETH Zurich
939:PhyloQuart
934:I. Letunic
480:S. Guindon
457:FastTree 2
452:G.J. Olsen
435:Jeon, Y.S.
394:Dendroscope
255:BioNumerics
110:David Reich
81:Description
4154:Categories
3770:Cladistics
3698:A list of
3079:2112.09755
2622:1712.06442
2511:Cladistics
2319:: e36178.
2099:1908.08623
1576:(1): 294.
1454:References
1435:I. Holmes
1352:Distance (
1301:Treefinder
1295:E. Wright
1266:TreeAlign
1209:SplitsTree
1194:Splatche3
1107:RAxML-HPC
1093:QuickTree
1065:ProtTest3
1060:M. Arenas
805:ParaPhylo
725:MorphoBank
644:MetaPIGA2
443:fastDNAml
116:AncesTree
93:ADMIXTOOLS
37:cladistics
4107:Supertree
4071:Polyphyly
4066:Paraphyly
4061:Monophyly
4033:Apomorphy
4013:Primitive
3956:PhyloCode
3838:Cladogram
3645:1367-4803
3418:retracted
3410:retracted
3268:1367-4803
2984:1367-4803
2945:2041-210X
2849:1076-836X
2702:2041-210X
2582:1367-4803
2492:1367-4803
2435:1553-7358
2335:196180156
2003:1934-340X
1972:264500732
1419:K. Nixon
1410:Winclada
1282:TreeLine
1186:SOWH test
1165:SimPlot++
1121:RAxML-NG
1079:PyCogent
1023:ProtEvol
1009:ProtASR2
953:PhyloWGS
948:V. Berry
893:phyclust
863:phangorn
814:Hellmuth
770:A. Roehl
626:Mesquite
485:Geneious
471:fitmodel
426:EzEditor
365:CoalEvol
149:R-Project
130:AliGROOVE
4126:Category
4029:Derived
3775:Taxonomy
3692:Another
3653:32573652
3604:33972780
3553:22675075
3504:11934758
3463:11448889
3397:26542699
3378:15222900
3327:16221896
3286:31077292
3229:26231182
3096:35451456
3051:31070718
3002:34450622
2898:28174903
2800:20156990
2759:21169378
2710:86694418
2659:25646426
2590:11524383
2541:76652345
2533:34875801
2453:34492010
2386:33335719
2360:: 1309.
2294:23418397
2245:25371430
2196:20224823
2155:PLOS One
2135:24425826
2060:22780991
2019:34156490
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