CAM: an alignment-free method to recover phylogenies using codon aversion motifs.

ABSTRACT:

Background

Common phylogenomic approaches for recovering phylogenies are often time-consuming and require annotations for orthologous gene relationships that are not always available. In contrast, alignment-free phylogenomic approaches typically use structure and oligomer frequencies to calculate pairwise distances between species. We have developed an approach to quickly calculate distances between species based on codon aversion.

Methods

Utilizing a novel alignment-free character state, we present CAM, an alignment-free approach to recover phylogenies by comparing differences in codon aversion motifs (i.e., the set of unused codons within each gene) across all genes within a species. Synonymous codon usage is non-random and differs between organisms, between genes, and eve

SUBMITTER: Miller JB 

PROVIDER: S-EPMC6555396 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature