ImOSM: intermittent evolution and robustness of phylogenetic methods.

ABSTRACT: Among the criteria to evaluate the performance of a phylogenetic method, robustness to model violation is of particular practical importance as complete a priori knowledge of evolutionary processes is typically unavailable. For studies of robustness in phylogenetic inference, a utility to add well-defined model violations to the simulated data would be helpful. We therefore introduce ImOSM, a tool to imbed intermittent evolution as model violation into an alignment. Intermittent evolution refers to extra substitutions occurring randomly on branches of a tree, thus changing alignment site patterns. This means that the extra substitutions are placed on the tree after the typical process of sequence evolution is completed. We then study the robustness of widely used phylogenetic methods: maxi

SUBMITTER: Thi Nguyen MA 

PROVIDER: S-EPMC3258038 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature