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RERconverge: an R Package for Associating Evolutionary Rates with Convergent Traits

Overview
Journal Bioinformatics
Publisher Oxford University Press
Specialty Biology
Date 2019 Jun 14
PMID 31192356
Citations 60
Authors
Amanda Kowalczyk
Wynn K Meyer
Raghavendran Partha
Weiguang Mao
Nathan L Clark
Maria Chikina
Affiliations
Soon will be listed here.
Abstract

Motivation: When different lineages of organisms independently adapt to similar environments, selection often acts repeatedly upon the same genes, leading to signatures of convergent evolutionary rate shifts at these genes. With the increasing availability of genome sequences for organisms displaying a variety of convergent traits, the ability to identify genes with such convergent rate signatures would enable new insights into the molecular basis of these traits.

Results: Here we present the R package RERconverge, which tests for association between relative evolutionary rates of genes and the evolution of traits across a phylogeny. RERconverge can perform associations with binary and continuous traits, and it contains tools for visualization and enrichment analyses of association results.

Availability And Implementation: RERconverge source code, documentation and a detailed usage walk-through are freely available at https://github.com/nclark-lab/RERconverge. Datasets for mammals, Drosophila and yeast are available at https://bit.ly/2J2QBnj.

Supplementary Information: Supplementary data are available at Bioinformatics online.

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