Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories.

ABSTRACT: Genomic evolution can be highly heterogeneous. Here, we introduce a new framework to simulate genome-wide sequence evolution under a variety of substitution models that may change along the genome and the phylogeny, following complex multispecies coalescent histories that can include recombination, demographics, longitudinal sampling, population subdivision/species history, and migration. A key aspect of our simulation strategy is that the heterogeneity of the whole evolutionary process can be parameterized according to statistical prior distributions specified by the user. We used this framework to carry out a study of the impact of variable codon frequencies across genomic regions on the estimation of the genome-wide nonsynonymous/synonymous ratio. We found that both variable codon frequ

SUBMITTER: Arenas M 

PROVIDER: S-EPMC3995339 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature