RT Journal Article
SR Electronic
T1 RERconverge: an R package for associating evolutionary rates with convergent traits
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 451138
DO 10.1101/451138
A1 Amanda Kowalczyk
A1 Wynn K Meyer
A1 Raghavendran Partha
A1 Weiguang Mao
A1 Nathan L Clark
A1 Maria Chikina
YR 2018
UL http://biorxiv.org/content/early/2018/10/23/451138.abstract
AB 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: 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.Contact: mchikina{at}pitt.eduSupplementary information: Supplementary information, containing detailed vignettes for usage of RERconverge, are available at Bioinformatics online.