Now showing items 1-6 of 6

    • 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 Biempica, 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 ...