publication . Other literature type . Article . Preprint . 2019

ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models

Darriba, Diego; Posada, David; Kozlov, Alexey M; Stamatakis, Alexandros; Morel, Benoit; Flouri, Tomas;
Open Access
  • Published: 22 Apr 2019
  • Publisher: Oxford University Press (OUP)
Abstract
<jats:title>Abstract</jats:title><jats:p>ModelTest-NG is a re-implementation from scratch of jModelTest and ProtTest, two popular tools for selecting the best-fit nucleotide and amino acid substitution models, respectively. ModelTest-NG is one to two orders of magnitude faster than jModelTest and ProtTest but equally accurate, and introduces several new features, such as ascertainment bias correction, mixture and FreeRate models, or the automatic processing of partitioned datasets. ModelTest-NG is available under a GNU GPL3 license at <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/ddarriba/modeltest">...
Subjects
free text keywords: phylogenetic model selection, high-performance computing, efficient algorithms, phylogenetic inference, DATA processing & computer science, ddc:004, Genetics, Ecology, Evolution, Behavior and Systematics, Molecular Biology, Resources
25 references, page 1 of 2

Abadi S, Azouri D, Pupko T, Mayrose I.2019 Model selection may not be a mandatory step for phylogeny reconstruction. Nat Commun. 10(1):934.30804347 [OpenAIRE] [PubMed]

Akaike H.1974 A new look at the statistical model identification. IEEE Trans Automat Contr. 19(6):716–723.

Arbiza L, Patricio M, Dopazo H, Posada D.2011 Genome-wide heterogeneity of nucleotide substitution model fit. Genome Biol Evol. 3:896–908.21824869 [OpenAIRE] [PubMed]

Buckley TR.2002 Model misspecification and probabilistic tests of topology: evidence from empirical data sets. Syst Biol. 51(3):509–523.12079647 [PubMed]

Buckley TR, Cunningham CW.2002 The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support. Mol Biol Evol. 19(4):394–405.11919280 [PubMed]

Darriba D, Taboada GL, Doallo R, Posada D.2011 ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27(8):1164–1165.21335321 [OpenAIRE] [PubMed]

Darriba D, Taboada GL, Doallo R, Posada D.2012 jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 9(8):772–772.

Guindon O, Gascuel S.2003 A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52(5):696–704.14530136 [OpenAIRE] [PubMed]

Hoff M, Orf S, Riehm B, Darriba D, Stamatakis A.2016 Does the choice of nucleotide substitution models matter topologically?BMC Bioinformatics 17(1):143.27009141 [OpenAIRE] [PubMed]

Kalyaanamoorthy S, Minh BQ, Wong TK, von Haeseler A, Jermiin LS.2017 Modelfinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 14(6):587.28481363 [OpenAIRE] [PubMed]

Kobert K, Stamatakis A, Flouri T.2017 Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations. Syst Biol. 66(2):205–217.27576546 [OpenAIRE] [PubMed]

Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. Forthcoming 2019 RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics pii: btz305.

Le SQ, Dang CC, Gascuel O.2012 Modeling protein evolution with several amino acid replacement matrices depending on site rates. Mol Biol Evol. 29(10):2921–2936.22491036 [OpenAIRE] [PubMed]

Lefort V, Longueville J-E, Gascuel O.2017 SMS: Smart Model Selection in PhyML. Mol Biol Evol. 34(9):2422–2424.28472384 [OpenAIRE] [PubMed]

Lemmon AR, Moriarty EC.2004 The importance of proper model assumption in Bayesian phylogenetic. Syst Biol. 53(2):265–277.15205052 [PubMed]

25 references, page 1 of 2
Abstract
<jats:title>Abstract</jats:title><jats:p>ModelTest-NG is a re-implementation from scratch of jModelTest and ProtTest, two popular tools for selecting the best-fit nucleotide and amino acid substitution models, respectively. ModelTest-NG is one to two orders of magnitude faster than jModelTest and ProtTest but equally accurate, and introduces several new features, such as ascertainment bias correction, mixture and FreeRate models, or the automatic processing of partitioned datasets. ModelTest-NG is available under a GNU GPL3 license at <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/ddarriba/modeltest">...
Subjects
free text keywords: phylogenetic model selection, high-performance computing, efficient algorithms, phylogenetic inference, DATA processing & computer science, ddc:004, Genetics, Ecology, Evolution, Behavior and Systematics, Molecular Biology, Resources
25 references, page 1 of 2

Abadi S, Azouri D, Pupko T, Mayrose I.2019 Model selection may not be a mandatory step for phylogeny reconstruction. Nat Commun. 10(1):934.30804347 [OpenAIRE] [PubMed]

Akaike H.1974 A new look at the statistical model identification. IEEE Trans Automat Contr. 19(6):716–723.

Arbiza L, Patricio M, Dopazo H, Posada D.2011 Genome-wide heterogeneity of nucleotide substitution model fit. Genome Biol Evol. 3:896–908.21824869 [OpenAIRE] [PubMed]

Buckley TR.2002 Model misspecification and probabilistic tests of topology: evidence from empirical data sets. Syst Biol. 51(3):509–523.12079647 [PubMed]

Buckley TR, Cunningham CW.2002 The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support. Mol Biol Evol. 19(4):394–405.11919280 [PubMed]

Darriba D, Taboada GL, Doallo R, Posada D.2011 ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27(8):1164–1165.21335321 [OpenAIRE] [PubMed]

Darriba D, Taboada GL, Doallo R, Posada D.2012 jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 9(8):772–772.

Guindon O, Gascuel S.2003 A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52(5):696–704.14530136 [OpenAIRE] [PubMed]

Hoff M, Orf S, Riehm B, Darriba D, Stamatakis A.2016 Does the choice of nucleotide substitution models matter topologically?BMC Bioinformatics 17(1):143.27009141 [OpenAIRE] [PubMed]

Kalyaanamoorthy S, Minh BQ, Wong TK, von Haeseler A, Jermiin LS.2017 Modelfinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 14(6):587.28481363 [OpenAIRE] [PubMed]

Kobert K, Stamatakis A, Flouri T.2017 Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations. Syst Biol. 66(2):205–217.27576546 [OpenAIRE] [PubMed]

Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. Forthcoming 2019 RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics pii: btz305.

Le SQ, Dang CC, Gascuel O.2012 Modeling protein evolution with several amino acid replacement matrices depending on site rates. Mol Biol Evol. 29(10):2921–2936.22491036 [OpenAIRE] [PubMed]

Lefort V, Longueville J-E, Gascuel O.2017 SMS: Smart Model Selection in PhyML. Mol Biol Evol. 34(9):2422–2424.28472384 [OpenAIRE] [PubMed]

Lemmon AR, Moriarty EC.2004 The importance of proper model assumption in Bayesian phylogenetic. Syst Biol. 53(2):265–277.15205052 [PubMed]

25 references, page 1 of 2
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