• DocumentCode
    2998491
  • Title

    SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model

  • Author

    Schabauer, H. ; Valle, M. ; Pacher, Christoph ; Stockinger, H. ; Stamatakis, Alexandros ; Robinson-Rechavi, M. ; Ziheng Yang ; Salamin, N.

  • fYear
    2012
  • fDate
    21-25 May 2012
  • Firstpage
    706
  • Lastpage
    714
  • Abstract
    CodeML (part of the PAML package) implements a maximum likelihood-based approach to detect positive selection on a specific branch of a given phylogenetic tree. While CodeML is widely used, it is very compute-intensive. We present SlimCodeML, an optimized version of CodeML for the branch-site model. Our performance analysis shows that SlimCodeML substantially outperforms CodeML (up to 9.38 times faster), especially for large-scale genomic analyses.
  • Keywords
    biology computing; genomics; maximum likelihood estimation; trees (mathematics); PAML package; SlimCodeML; branch-site model; large-scale genomic analyses; maximum likelihood-based approach; phylogenetic tree; Bioinformatics; Computational modeling; Genomics; Matrices; Phylogeny; Symmetric matrices; Vectors; codon models; likelihood computation; molecular evolution; phylogenetics; scientific computing;
  • fLanguage
    English
  • Publisher
    ieee
  • Conference_Titel
    Parallel and Distributed Processing Symposium Workshops & PhD Forum (IPDPSW), 2012 IEEE 26th International
  • Conference_Location
    Shanghai
  • Print_ISBN
    978-1-4673-0974-5
  • Type

    conf

  • DOI
    10.1109/IPDPSW.2012.88
  • Filename
    6270710
    • Link To Document
    https://search.isc.ac/dl/search/defaultta.aspx?DTC=49&DC=2998491