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

ABSTRACT:

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 substantiall

SUBMITTER: Valle M 

PROVIDER: S-EPMC3982156 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature