RERconverge: an R package for associating evolutionary rates with convergent traits.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 11 2019
01 11 2019
Historique:
received:
30
11
2018
revised:
08
04
2019
accepted:
06
06
2019
pubmed:
14
6
2019
medline:
25
6
2020
entrez:
14
6
2019
Statut:
ppublish
Résumé
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. 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. 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 data are available at Bioinformatics online.
Identifiants
pubmed: 31192356
pii: 5514536
doi: 10.1093/bioinformatics/btz468
pmc: PMC6853647
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4815-4817Subventions
Organisme : NHGRI NIH HHS
ID : R01 HG009299
Pays : United States
Organisme : NIBIB NIH HHS
ID : T32 EB009403
Pays : United States
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Références
Mol Biol Evol. 2011 Jan;28(1):729-44
pubmed: 20926596
Mol Biol Evol. 2016 Aug;33(8):2135-50
pubmed: 27222536
Science. 2018 Aug 10;361(6402):591-594
pubmed: 30093596
Mol Biol Evol. 2007 Aug;24(8):1586-91
pubmed: 17483113
Cell Rep. 2012 Oct 25;2(4):817-23
pubmed: 23022484
Mol Biol Evol. 2016 Sep;33(9):2182-92
pubmed: 27329977
Curr Biol. 2010 Jan 26;20(2):R55-6
pubmed: 20129037
Mol Biol Evol. 2019 May 1;36(5):1086-1100
pubmed: 30851112
Elife. 2017 Oct 16;6:
pubmed: 29035697
Mol Biol Evol. 2019 Aug 1;36(8):1817-1830
pubmed: 31077321
Proc Natl Acad Sci U S A. 2012 Mar 20;109(12):4556-61
pubmed: 22392995
Pigment Cell Melanoma Res. 2012 Jul;25(4):411-33
pubmed: 22578174