{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T09:30:12Z","timestamp":1785576612053,"version":"3.56.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2018,11,6]],"date-time":"2018-11-06T00:00:00Z","timestamp":1541462400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100011102","name":"European Union Seventh Framework Programme","doi-asserted-by":"publisher","award":["FP7\/2007-2013"],"award-info":[{"award-number":["FP7\/2007-2013"]}],"id":[{"id":"10.13039\/100011102","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"PhD Fellowship of the Research Foundation\u2014Flanders"},{"DOI":"10.13039\/501100003130","name":"FWO","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>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 colinearity. Despite the increased interest in WGDs and the acknowledgment 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 colinearity analysis workflows together with tools for modeling and visualization, rendering these analyses accessible to genomics researchers in a convenient manner.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>wgd is free and open source software implemented in Python and is available at https:\/\/github.com\/arzwa\/wgd.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty915","type":"journal-article","created":{"date-parts":[[2018,11,5]],"date-time":"2018-11-05T20:13:13Z","timestamp":1541448793000},"page":"2153-2155","source":"Crossref","is-referenced-by-count":271,"title":["wgd\u2014simple command line tools for the analysis of ancient whole-genome duplications"],"prefix":"10.1093","volume":"35","author":[{"given":"Arthur","family":"Zwaenepoel","sequence":"first","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University"},{"name":"Center for Plant Systems Biology, VIB"},{"name":"Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yves","family":"Van de Peer","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University"},{"name":"Center for Plant Systems Biology, VIB"},{"name":"Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium"},{"name":"Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,11,6]]},"reference":[{"key":"2023012713225967600_bty915-B1","doi-asserted-by":"crossref","first-page":"1667","DOI":"10.1105\/tpc.021345","article-title":"Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes","volume":"16","author":"Blanc","year":"2004","journal-title":"Plant Cell"},{"key":"2023012713225967600_bty915-B2","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1101\/gr.4825606","article-title":"Widespread genome duplications throughout the history of flowering plants","volume":"16","author":"Cui","year":"2006","journal-title":"Genome Res."},{"key":"2023012713225967600_bty915-B3","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1126\/science.290.5494.1151","article-title":"The evolutionary fate and consequences of duplicate genes","volume":"290","author":"Lynch","year":"2000","journal-title":"Science"},{"key":"2023012713225967600_bty915-B4","first-page":"2825","article-title":"Scikit-learn: machine learning in Python","volume":"12","author":"Pedregosa","year":"2011","journal-title":"J. Mach. Learn. Res."},{"key":"2023012713225967600_bty915-B5","doi-asserted-by":"crossref","first-page":"e11","DOI":"10.1093\/nar\/gkr955","article-title":"i-ADHoRe 3.0: fast and sensitive detection of genomic homology in extremely large data sets","volume":"40","author":"Proost","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012713225967600_bty915-B6","first-page":"2882","article-title":"Assessing the performance of Ks plots for detecting ancient whole genome duplications","volume":"10","author":"Tiley","year":"2018","journal-title":"Genome Biol. Evol."},{"key":"2023012713225967600_bty915-B7","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1038\/nrg1449","article-title":"Computational approaches to unveiling ancient genome duplications","volume":"5","author":"Van de Peer","year":"2004","journal-title":"Nat. Rev. Genet."},{"key":"2023012713225967600_bty915-B8","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nrg.2017.26","article-title":"The evolutionary significance of polyploidy","volume":"18","author":"Van de Peer","year":"2017","journal-title":"Nat. Rev. Genet."},{"key":"2023012713225967600_bty915-B9","unstructured":"van Dongen\n       \u00a0S.\n           (2000) Graph Clustering by Flow Simulation. PhD Thesis, University of Utrecht, Utrecht, The Netherlands."},{"key":"2023012713225967600_bty915-B10","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1093\/molbev\/mss214","article-title":"Inference of genome duplications from age distributions revisited","volume":"30","author":"Vanneste","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"2023012713225967600_bty915-B11","doi-asserted-by":"crossref","first-page":"1334","DOI":"10.1101\/gr.168997.113","article-title":"Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary","volume":"24","author":"Vanneste","year":"2014","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/12\/2153\/48934898\/bioinformatics_35_12_2153.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/12\/2153\/48934898\/bioinformatics_35_12_2153.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T14:16:48Z","timestamp":1674829008000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/12\/2153\/5162749"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,11,6]]},"references-count":11,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2019,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty915","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,6]]},"published":{"date-parts":[[2018,11,6]]}}}