Polytomy refinement for the correction of dubious duplications in gene trees.

ABSTRACT:

Motivation

Large-scale methods for inferring gene trees are error-prone. Correcting gene trees for weakly supported features often results in non-binary trees, i.e. trees with polytomies, thus raising the natural question of refining such polytomies into binary trees. A feature pointing toward potential errors in gene trees are duplications that are not supported by the presence of multiple gene copies.

Results

We introduce the problem of refining polytomies in a gene tree while minimizing the number of created non-apparent duplications in the resulting tree. We show that this problem can be described as a graph-theoretical optimization problem. We provide a bounded heuristic with guaranteed optimality for well-characterized instances. We apply our algorithm to a set of ray-

SUBMITTER: Lafond M 

PROVIDER: S-EPMC4147916 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature