Listar GI-GAC - Artigos por autor "Darriba, Diego"

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    • Does the choice of nucleotide substitution models matter topologically? 

      Hoff, Michael; Orf, Stefan; Riehm, Benedikt; Darriba, Diego; Stamatakis, Alexandros (BioMed Central Ltd., 2016-03-24)
      [Abstract] Background: In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available an open-source code for testing all ...

    • High-performance computing selection of models of DNA substitution for multicore clusters 

      Darriba, Diego; López Taboada, Guillermo; Doallo, Ramón; Posada, David (Sage Publications Ltd., 2014)
      [Abstract] This paper presents the high-performance computing (HPC) support of jModelTest2, the most popular bioinformatic tool for the statistical selection of models of DNA substitution. As this can demand vast computational ...

    • jmodeltest.org: selection of nucleotide substitution models on the cloud 

      Santorum, Jose Manuel; Darriba, Diego; López Taboada, Guillermo; Posada, David (Oxford University Press, 2014)
      [Abstract] The selection of models of nucleotide substitution is one of the major steps of modern phylogenetic analysis. Different tools exist to accomplish this task, among which jModelTest 2 (jMT2) is one of the most ...

    • 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 (Oxford University Press, 2019-08-21)
      [Abstract] ModelTest-NG is a reimplementation 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 ...

    • Prediction of missing sequences and branch lengths in phylogenomic data 

      Darriba, Diego; Weiß, Michael; Stamatakis, Alexandros (Oxford University Press, 2016-01-05)
      [Abstract] Motivation: The presence of missing data in large-scale phylogenomic datasets has negative effects on the phylogenetic inference process. One effect that is caused by alignments with missing per-gene or per-partition ...

    • The Phylogenetic Likelihood Library 

      Flouri, Tomas; Izquierdo-Carrasco, F.; Darriba, Diego; Aberer, Andre J.; Nguyen, Lam-Tung; Minh, B.Q.; Haeseler, Arndt von; Stamatakis, Alexandros (Oxford University Press, 2015-03-01)
      [Abstract] We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements ...

    • The Wall Lizards of the Balkan Peninsula: Tackling Questions at the Interphase of Phylogenomics and Population Genomics 

      Psonis, Nikolaos; Antioniou, Aglaia; Karameta, Emmanouela; Darriba, Diego; Stamatakis, Alexandros; Lymberakis, Petros; Poulakakis, Nikos (Elsevier, 2021)
      [Abstract] Wall lizards of the genus Podarcis (Sauria, Lacertidae) are the predominant reptile group in southern Europe, including 24 recognized species. Mitochondrial DNA data have shown that, with the exception of P. ...