HPC selection of models of DNA substitution

Authors:
Diego Darriba;Guillermo L. Taboada;Ramón Doallo;David Posada
Affiliations:
University of A Coruña, A Coruña, Spain and University of Vigo, Vigo, Spain;University of A Coruña, A Coruña, Spain;University of A Coruña, A Coruña, Spain;University of Vigo, Vigo, Spain
Venue:
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
Year:
2011

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Abstract

Statistical model selection has become an essential step for the estimation of phylogenies from DNA sequence alignments. The program jModelTest offers different strategies to identify best-fit models for the data at hand, but for large DNA alignments, this task can demand vast computational resources. This paper presents a High Performance Computing (HPC) adaptation of jModelTest for shared memory multi-core systems and distributed memory cluster platforms. The performance evaluation of this HPC version on a shared memory system and on a cluster shows significant performance advantages, with speedups up to 39. This could represent a reduction in the execution time of some analyses from almost one day to half an hour.