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jModelTest 2: more models, new heuristics and parallel computing

Nature Methods volume 9, page 772 (2012) Cite this article

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To the Editor:

The statistical selection of best-fit models of nucleotide substitution is routine in the phylogenetic analysis of DNA sequence alignments1. With the advent of next-generation sequencing technologies, most researchers are moving from phylogenetics to phylogenomics, in which large sequence alignments typically include hundreds or thousands of loci. Phylogenetic resources therefore need to be adapted to a high-performance computing paradigm so as to allow demanding analyses at the genomic level. Here we introduce jModelTest 2, a program for nucleotide-substitution model selection that incorporates more models, new heuristics, efficient technical optimizations and parallel computing.

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Figure 1: Benchmarking of the filtering heuristic in jModelTest 2.

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Acknowledgements

This work was financially supported by the European Research Council (ERC-2007-Stg 203161-PHYGENOM to D.P.), Spanish Ministry of Science and Education (BFU2009-08611 to D.P.) and Xunta de Galicia (Galician Thematic Networks RGB 2010/90 to D.P. and GHPC2 2010/53 to R.D.).

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Authors and Affiliations

  1. Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain

    Diego Darriba & David Posada

  2. Computer Architecture Group, University of A Coruña, A Coruña, Spain

    Diego Darriba, Guillermo L Taboada & Ramón Doallo

Authors
  1. Diego Darriba
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  2. Guillermo L Taboada
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  3. Ramón Doallo
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  4. David Posada
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Correspondence to David Posada.

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The authors declare no competing financial interests.

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Darriba, D., Taboada, G., Doallo, R. et al. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9, 772 (2012). https://doi.org/10.1038/nmeth.2109

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