Optimization strategies for fast detection of positive selection on phylogenetic trees.

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Ressource 1Télécharger: BIB_EE03C80A1584.P001.pdf (550.58 [Ko])
Etat: Serval
Version: de l'auteur
ID Serval
serval:BIB_EE03C80A1584
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Optimization strategies for fast detection of positive selection on phylogenetic trees.
Périodique
Bioinformatics
Auteur(s)
Valle M., Schabauer H., Pacher C., Stockinger H., Stamatakis A., Robinson-Rechavi M., Salamin N.
ISSN
1367-4811 (Electronic)
ISSN-L
1367-4803
Statut éditorial
Publié
Date de publication
2014
Peer-reviewed
Oui
Volume
30
Numéro
8
Pages
1129-1137
Langue
anglais
Résumé
MOTIVATION: The detection of positive selection is widely used to study gene and genome evolution, but its application remains limited by the high computational cost of existing implementations. We present a series of computational optimizations for more efficient estimation of the likelihood function on large-scale phylogenetic problems. We illustrate our approach using the branch-site model of codon evolution.
RESULTS: We introduce novel optimization techniques that substantially outperform both CodeML from the PAML package and our previously optimized sequential version SlimCodeML. These techniques can also be applied to other likelihood-based phylogeny software. Our implementation scales well for large numbers of codons and/or species. It can therefore analyse substantially larger datasets than CodeML. We evaluated FastCodeML on different platforms and measured average sequential speedups of FastCodeML (single-threaded) versus CodeML of up to 5.8, average speedups of FastCodeML (multi-threaded) versus CodeML on a single node (shared memory) of up to 36.9 for 12 CPU cores, and average speedups of the distributed FastCodeML versus CodeML of up to 170.9 on eight nodes (96 CPU cores in total).Availability and implementation: ftp://ftp.vital-it.ch/tools/FastCodeML/.
CONTACT: selectome@unil.ch or nicolas.salamin@unil.ch.
Pubmed
Web of science
Création de la notice
06/01/2014 17:35
Dernière modification de la notice
03/03/2018 22:32
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