SWAMP: Sliding Window Alignment Masker for PAML.

ABSTRACT: With the greater availability of genetic data, large genome-wide scans for positive selection increasingly incorporate data from a range of sources. These data sets may be derived from different sequencing methods, each of which has potential sources of error. Sequencing errors, compounded by alignment errors, greatly increase the number of false positives in tests for adaptive evolution. Genome-wide analyses often fail to fully address these issues or to provide sufficient detail on postalignment masking/filtering. Here, we introduce a Sliding Window Alignment Masker for Phylogenetic Analysis by Maximum Likelihood (SWAMP) that scans multiple-sequence alignments for short regions enriched with unreasonably high rates of nonsynonymous substitutions caused, for example, by sequence or alignm

SUBMITTER: Harrison PW 

PROVIDER: S-EPMC4251194 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature