publication . Article . Other literature type . Preprint . 2018

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.

Alexey M. Kozlov; Diego Darriba; Tomáš Flouri; Benoit Morel; Alexandros Stamatakis;
Open Access English
  • Published: 18 Oct 2018
  • Publisher: Oxford University Press (OUP)
  • Country: United Kingdom
Abstract
<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Motivation</jats:title> <jats:p>Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree under the popular maximum likelihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>We present RAxML-NG, a from-scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML-NG offers improved accuracy, flexibil...
Subjects
free text keywords: Statistics and Probability, Computational Theory and Mathematics, Biochemistry, Molecular Biology, Computational Mathematics, Computer Science Applications, Applications Notes, Phylogenetics
18 references, page 1 of 2

Baele,G. et al. (2010) Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences. J. Mol. Evol., 71, 34-50.

Barbera,P. et al. (2018) EPA-ng: massively parallel evolutionary placement of genetic sequences. Syst. Biol., 68, 365-369. [OpenAIRE]

Biczok,R. et al. (2017) Two Cþþ libraries for counting trees on a phylogenetic terrace. Bioinformatics, 34, 3399-3401. [OpenAIRE]

Fletcher,R. (1987) Practical Methods of Optimization. Vol. 1. John Wiley & Sons, Chichester, New York.

Guindon,S. et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol., 59, 307-321.

Kobert,K. et al. (2014) The divisible load balance problem and its application to phylogenetic inference. In: Brown,D. and Morgenstern,B. (eds) Algorithms in Bioinformatics, Volume 8701 of Lecture Notes in Computer Science. Springer, Berlin Heidelberg, pp. 204-216. [OpenAIRE]

Kobert,K. et al. (2017) Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations. Syst. Biol., 66, 205-217.

Kozlov,A.M. et al. (2015) ExaML version 3: a tool for phylogenomic analyses on supercomputers. Bioinformatics, 31, 2577-2579. [OpenAIRE]

Le,S.Q. et al. (2008) Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics, 24, 2317-2323.

Le,S.Q. et al. (2012) Modeling protein evolution with several amino acid replacement matrices depending on site rates. Mol. Biol. Evol., 29, 2921-2936.

Lemoine,F. et al. (2018) Renewing Felsensteinen phylogenetic bootstrap in the era of big data. Nature, 556, 452-456. [OpenAIRE]

Nguyen,L.-T. et al. (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol., 32, 268-274. [OpenAIRE]

Price,M.N. et al. (2010) FastTree 2 - approximately maximum-likelihood trees for large alignments. PLoS One, 5, 1-10.

Sanderson,M.J. et al. (2011) Terraces in phylogenetic tree space. Science, 333, 448-450.

Stamatakis,A. (2006) Phylogenetic models of rate heterogeneity: a high performance computing perspective. In: Proceedings of IPDPS2006, HICOMB Workshop, Proceedings on CD, IEEE, Rhodos, Greece.

18 references, page 1 of 2
Abstract
<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Motivation</jats:title> <jats:p>Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree under the popular maximum likelihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>We present RAxML-NG, a from-scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML-NG offers improved accuracy, flexibil...
Subjects
free text keywords: Statistics and Probability, Computational Theory and Mathematics, Biochemistry, Molecular Biology, Computational Mathematics, Computer Science Applications, Applications Notes, Phylogenetics
18 references, page 1 of 2

Baele,G. et al. (2010) Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences. J. Mol. Evol., 71, 34-50.

Barbera,P. et al. (2018) EPA-ng: massively parallel evolutionary placement of genetic sequences. Syst. Biol., 68, 365-369. [OpenAIRE]

Biczok,R. et al. (2017) Two Cþþ libraries for counting trees on a phylogenetic terrace. Bioinformatics, 34, 3399-3401. [OpenAIRE]

Fletcher,R. (1987) Practical Methods of Optimization. Vol. 1. John Wiley & Sons, Chichester, New York.

Guindon,S. et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol., 59, 307-321.

Kobert,K. et al. (2014) The divisible load balance problem and its application to phylogenetic inference. In: Brown,D. and Morgenstern,B. (eds) Algorithms in Bioinformatics, Volume 8701 of Lecture Notes in Computer Science. Springer, Berlin Heidelberg, pp. 204-216. [OpenAIRE]

Kobert,K. et al. (2017) Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations. Syst. Biol., 66, 205-217.

Kozlov,A.M. et al. (2015) ExaML version 3: a tool for phylogenomic analyses on supercomputers. Bioinformatics, 31, 2577-2579. [OpenAIRE]

Le,S.Q. et al. (2008) Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics, 24, 2317-2323.

Le,S.Q. et al. (2012) Modeling protein evolution with several amino acid replacement matrices depending on site rates. Mol. Biol. Evol., 29, 2921-2936.

Lemoine,F. et al. (2018) Renewing Felsensteinen phylogenetic bootstrap in the era of big data. Nature, 556, 452-456. [OpenAIRE]

Nguyen,L.-T. et al. (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol., 32, 268-274. [OpenAIRE]

Price,M.N. et al. (2010) FastTree 2 - approximately maximum-likelihood trees for large alignments. PLoS One, 5, 1-10.

Sanderson,M.J. et al. (2011) Terraces in phylogenetic tree space. Science, 333, 448-450.

Stamatakis,A. (2006) Phylogenetic models of rate heterogeneity: a high performance computing perspective. In: Proceedings of IPDPS2006, HICOMB Workshop, Proceedings on CD, IEEE, Rhodos, Greece.

18 references, page 1 of 2
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