Evaluating rare amino acid substitutions (RGC_CAMs) in a yeast model clade.

ABSTRACT: When inferring phylogenetic relationships, not all sites in a sequence alignment are equally informative. One recently proposed approach that takes advantage of this inequality relies on sites that contain amino acids whose replacement requires multiple substitutions. Identifying these so-called RGC_CAM substitutions (after Rare Genomic Changes as Conserved Amino acids-Multiple substitutions) requires that, first, at any given site in the amino acid sequence alignment, there must be a minimum of two different amino acids; second, each amino acid must be present in at least two taxa; and third, the amino acids must require a minimum of two nucleotide substitutions to replace each other. Although theory suggests that RGC_CAM substitutions are expected to be rare and less likely to be homopla

SUBMITTER: Polzin K 

PROVIDER: S-EPMC3956930 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature