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.
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;
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
DOI :
10.1109/IPDPSW.2012.88
