{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T14:21:47Z","timestamp":1784730107693,"version":"3.55.0"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,8,18]],"date-time":"2021-08-18T00:00:00Z","timestamp":1629244800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"VIB and Ghent University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>We present ksrates, a user-friendly command-line tool to position ancient whole-genome duplication events with respect to speciation events in a phylogeny by comparing paralog and ortholog KS distributions derived from genomic or transcriptomic sequences, while adjusting for substitution rate differences among the lineages involved.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>ksrates is implemented in Python 3 and as a Nextflow pipeline. The source code, Singularity and Docker containers, documentation and tutorial are available via https:\/\/github.com\/VIB-PSB\/ksrates.<\/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\/btab602","type":"journal-article","created":{"date-parts":[[2021,8,17]],"date-time":"2021-08-17T07:47:25Z","timestamp":1629186445000},"page":"530-532","source":"Crossref","is-referenced-by-count":61,"title":["<i>ksrates<\/i>\n                    : positioning whole-genome duplications relative to speciation events in\n                    <i>K<\/i>\n                    S distributions"],"prefix":"10.1093","volume":"38","author":[{"given":"Cecilia","family":"Sensalari","sequence":"first","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent 9052, Belgium"},{"name":"VIB Center for Plant Systems Biology , Ghent 9052, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5341-136X","authenticated-orcid":false,"given":"Steven","family":"Maere","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent 9052, Belgium"},{"name":"VIB Center for Plant Systems Biology , Ghent 9052, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rolf","family":"Lohaus","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent 9052, Belgium"},{"name":"VIB Center for Plant Systems Biology , Ghent 9052, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,8,18]]},"reference":[{"key":"2023020108420205200_btab602-B1","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1093\/gbe\/evp040","article-title":"Paleopolyploidy in the Brassicales: analyses of the Cleome transcriptome elucidate the history of genome duplications in Arabidopsis and other Brassicales","volume":"1","author":"Barker","year":"2009","journal-title":"Genome Biol. 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