Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping.

ABSTRACT: Genes and genomes do not evolve similarly in all branches of the tree of life. Detecting and characterizing the heterogeneity in time, and between lineages, of the nucleotide (or amino acid) substitution process is an important goal of current molecular evolutionary research. This task is typically achieved through the use of non-homogeneous models of sequence evolution, which being highly parametrized and computationally-demanding are not appropriate for large-scale analyses. Here we investigate an alternative methodological option based on probabilistic substitution mapping. The idea is to first reconstruct the substitutional history of each site of an alignment under a homogeneous model of sequence evolution, then to characterize variations in the substitution process across lineages ba

SUBMITTER: Romiguier J 

PROVIDER: S-EPMC3313935 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature