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wgd-simple command line tools for the analysis of ancient whole genome duplications

Arthur Zwaenepoel (UGent) and Yves Van de Peer (UGent)
(2019) BIOINFORMATICS. 35(12). p.2153-2155
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Abstract
MOTIVATION: Ancient whole genome duplications (WGDs) have been uncovered in almost all major lineages of life on Earth and the search for traces or remnants of such events has become standard practice in most genome analyses. This is especially true for plants, where ancient WGDs are abundant. Common approaches to find evidence for ancient WGDs include the construction of KS distributions and the analysis of intragenomic co-linearity. Despite the increased interest in WGDs and the acknowledgement of their evolutionary importance, user-friendly and comprehensive tools for their analysis are lacking. Here, we present an easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides commonly used KS and co-linearity analysis workflows together with tools for modeling and visualization, rendering these analyses accessible to genomics researchers in a convenient manner. AVAILABILITY & IMPLEMENTATION: wgd is free and open source software implemented in Python and is available at https://github.com/arzwa/wgd. SUPPLEMENTARY INFORMATION: Supplementary methods are available at Bioinformatics online.
Keywords
Statistics and Probability, Computational Theory and Mathematics, Biochemistry, Molecular Biology, Computational Mathematics, Computer Science Applications

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Please use this url to cite or link to this publication:

MLA
Zwaenepoel, Arthur, and Yves Van de Peer. “Wgd-simple Command Line Tools for the Analysis of Ancient Whole Genome Duplications.” BIOINFORMATICS 35.12 (2019): 2153–2155. Print.
APA
Zwaenepoel, A., & Van de Peer, Y. (2019). wgd-simple command line tools for the analysis of ancient whole genome duplications. BIOINFORMATICS, 35(12), 2153–2155.
Chicago author-date
Zwaenepoel, Arthur, and Yves Van de Peer. 2019. “Wgd-simple Command Line Tools for the Analysis of Ancient Whole Genome Duplications.” Bioinformatics 35 (12): 2153–2155.
Chicago author-date (all authors)
Zwaenepoel, Arthur, and Yves Van de Peer. 2019. “Wgd-simple Command Line Tools for the Analysis of Ancient Whole Genome Duplications.” Bioinformatics 35 (12): 2153–2155.
Vancouver
1.
Zwaenepoel A, Van de Peer Y. wgd-simple command line tools for the analysis of ancient whole genome duplications. BIOINFORMATICS. 2019;35(12):2153–5.
IEEE
[1]
A. Zwaenepoel and Y. Van de Peer, “wgd-simple command line tools for the analysis of ancient whole genome duplications,” BIOINFORMATICS, vol. 35, no. 12, pp. 2153–2155, 2019.
@article{8584064,
  abstract     = {MOTIVATION: Ancient whole genome duplications (WGDs) have been uncovered in almost all major lineages of life on Earth and the search for traces or remnants of such events has become standard practice in most genome analyses. This is especially true for plants, where ancient WGDs are abundant. Common approaches to find evidence for ancient WGDs include the construction of KS distributions and the analysis of intragenomic co-linearity. Despite the increased interest in WGDs and the acknowledgement of their evolutionary importance, user-friendly and comprehensive tools for their analysis are lacking. Here, we present an easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides commonly used KS and co-linearity analysis workflows together with tools for modeling and visualization, rendering these analyses accessible to genomics researchers in a convenient manner.
AVAILABILITY & IMPLEMENTATION: wgd is free and open source software implemented in Python and is available at https://github.com/arzwa/wgd.
SUPPLEMENTARY INFORMATION: Supplementary methods are available at Bioinformatics online.},
  author       = {Zwaenepoel, Arthur and Van de Peer, Yves},
  issn         = {1367-4803},
  journal      = {BIOINFORMATICS},
  keywords     = {Statistics and Probability,Computational Theory and Mathematics,Biochemistry,Molecular Biology,Computational Mathematics,Computer Science Applications},
  language     = {eng},
  number       = {12},
  pages        = {2153--2155},
  title        = {wgd-simple command line tools for the analysis of ancient whole genome duplications},
  url          = {http://dx.doi.org/10.1093/bioinformatics/bty915},
  volume       = {35},
  year         = {2019},
}

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