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RERconverge: an R package for associating evolutionary rates with convergent traits

Amanda Kowalczyk, Wynn K Meyer, Raghavendran Partha, View ORCID ProfileWeiguang Mao, Nathan L Clark, Maria Chikina
doi: https://doi.org/10.1101/451138
Amanda Kowalczyk
1Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
2Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, PA, USA
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Wynn K Meyer
1Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
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Raghavendran Partha
1Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
2Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, PA, USA
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Weiguang Mao
1Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
2Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, PA, USA
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  • ORCID record for Weiguang Mao
Nathan L Clark
1Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
2Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, PA, USA
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Maria Chikina
1Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
2Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, PA, USA
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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: 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.edu

Supplementary information: Supplementary information, containing detailed vignettes for usage of RERconverge, are available at Bioinformatics online.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 23, 2018.
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RERconverge: an R package for associating evolutionary rates with convergent traits
Amanda Kowalczyk, Wynn K Meyer, Raghavendran Partha, Weiguang Mao, Nathan L Clark, Maria Chikina
bioRxiv 451138; doi: https://doi.org/10.1101/451138
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RERconverge: an R package for associating evolutionary rates with convergent traits
Amanda Kowalczyk, Wynn K Meyer, Raghavendran Partha, Weiguang Mao, Nathan L Clark, Maria Chikina
bioRxiv 451138; doi: https://doi.org/10.1101/451138

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