The duplication-loss small phylogeny problem: from cherries to trees.

ABSTRACT: The reconstruction of the history of evolutionary genome-wide events among a set of related organisms is of great biological interest since it can help to reveal the genomic basis of phenotypes. The sequencing of whole genomes faciliates the study of gene families that vary in size through duplication and loss events, like transfer RNA. However, a high sequence similarity often does not allow one to distinguish between orthologs and paralogs. Previous methods have addressed this difficulty by taking into account flanking regions of members of a family independently. We go one step further by inferring the order of genes of (a set of) families for ancestral genomes by considering the order of these genes on sequenced genomes. We present a novel branch-and-cut algorithm to solve the two spec

SUBMITTER: Andreotti S 

PROVIDER: S-EPMC3761417 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature