{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T15:48:40Z","timestamp":1779896920567,"version":"3.53.1"},"reference-count":15,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2021,5,21]],"date-time":"2021-05-21T00:00:00Z","timestamp":1621555200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Natural Sciences and Engineering Research Council of Canada","award":["RGPIN-2016-05585"],"award-info":[{"award-number":["RGPIN-2016-05585"]}]},{"name":"Natural Sciences and Engineering Research Council of Canada","award":["RGPIN-2019-0624"],"award-info":[{"award-number":["RGPIN-2019-0624"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Algorithms"],"abstract":"<jats:p>The RACCROCHE pipeline reconstructs ancestral gene orders and chromosomal contents of the ancestral genomes at all internal vertices of a phylogenetic tree. The strategy is to accumulate a very large number of generalized adjacencies, phylogenetically justified for each ancestor, to produce long ancestral contigs through maximum weight matching. It constructs chromosomes by counting the frequencies of ancestral contig co-occurrences on the extant genomes, clustering these for each ancestor and ordering them. The main objective of this paper is to closely simulate the evolutionary process giving rise to the gene content and order of a set of extant genomes (six distantly related monocots), and to assess to what extent an updated version of RACCROCHE can recover the artificial ancestral genome at the root of the phylogenetic tree relating to the simulated genomes.<\/jats:p>","DOI":"10.3390\/a14060160","type":"journal-article","created":{"date-parts":[[2021,5,21]],"date-time":"2021-05-21T13:15:15Z","timestamp":1621602915000},"page":"160","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Validation of Automated Chromosome Recovery in the Reconstruction of Ancestral Gene Order"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3316-2172","authenticated-orcid":false,"given":"Qiaoji","family":"Xu","sequence":"first","affiliation":[{"name":"Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON K1N 6N5, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4586-2347","authenticated-orcid":false,"given":"Lingling","family":"Jin","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4811-2231","authenticated-orcid":false,"given":"James H.","family":"Leebens-Mack","sequence":"additional","affiliation":[{"name":"Department of Plant Biology, University of Georgia, Athens, GA 30602, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8415-5189","authenticated-orcid":false,"given":"David","family":"Sankoff","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON K1N 6N5, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,5,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Perrin, A., Varr\u00e9, J.S., Blanquart, S., and Ouangraoua, A. 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