Titre
Optimization strategies for fast detection of positive selection on phylogenetic trees.
Type
article
Institution
UNIL/CHUV/Unisanté + institutions partenaires
Périodique
Auteur(s)
Valle, M.
Auteure/Auteur
Schabauer, H.
Auteure/Auteur
Pacher, C.
Auteure/Auteur
Stockinger, H.
Auteure/Auteur
Stamatakis, A.
Auteure/Auteur
Robinson-Rechavi, M.
Auteure/Auteur
Salamin, N.
Auteure/Auteur
Liens vers les personnes
ISSN
1367-4811
Statut éditorial
Publié
Date de publication
2014
Volume
30
Numéro
8
Première page
1129
Dernière page/numéro d’article
1137
Peer-reviewed
Oui
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.
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.
PID Serval
serval:BIB_EE03C80A1584
PMID
Open Access
Oui
Date de création
2014-01-06T15:35:31.376Z
Date de création dans IRIS
2025-05-21T05:27:45Z
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Nom
BIB_EE03C80A1584.P001.pdf
Version du manuscrit
preprint
Taille
550.58 KB
Format
Adobe PDF
PID Serval
serval:BIB_EE03C80A1584.P001
URN
urn:nbn:ch:serval-BIB_EE03C80A15849
Somme de contrôle
(MD5):db0543ccc34e0a5941991bc31c0f1543