Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference.

ABSTRACT:

Motivation

Accurate orthology inference is a fundamental step in many phylogenetics and comparative analysis. Many methods have been proposed, including OMA (Orthologous MAtrix). Yet substantial challenges remain, in particular in coping with fragmented genes or genes evolving at different rates after duplication, and in scaling to large datasets. With more and more genomes available, it is necessary to improve the scalability and robustness of orthology inference methods.

Results

We present improvements in the OMA algorithm: (i) refining the pairwise orthology inference step to account for same-species paralogs evolving at different rates, and (ii) minimizing errors in the pairwise orthology verification step by testing the consistency of pairwise distance estimates, which

SUBMITTER: Train CM 

PROVIDER: S-EPMC5870696 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature