{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T15:47:41Z","timestamp":1779896861767,"version":"3.53.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: A gene tree-species tree reconciliation explains the evolution of a gene tree within the species tree given a model of gene-family evolution. We describe ecceTERA, a program that implements a generic parsimony reconciliation algorithm, which accounts for gene duplication, loss and transfer (DTL) as well as speciation, involving sampled and unsampled lineages, within undated, fully dated or partially dated species trees. The ecceTERA reconciliation model and algorithm generalize or improve upon most published DTL parsimony algorithms for binary species trees and binary gene trees. Moreover, ecceTERA can estimate accurate species-tree aware gene trees using amalgamation.<\/jats:p>\n               <jats:p>Availability and implementation: ecceTERA is freely available under http:\/\/mbb.univ-montp2.fr\/MBB\/download_sources\/16__ecceTERA and can be run online at http:\/\/mbb.univ-montp2.fr\/MBB\/subsection\/softExec.php?soft=eccetera.<\/jats:p>\n               <jats:p>Contact: \u00a0celine.scornavacca@umontpellier.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw105","type":"journal-article","created":{"date-parts":[[2016,2,27]],"date-time":"2016-02-27T02:10:41Z","timestamp":1456539041000},"page":"2056-2058","source":"Crossref","is-referenced-by-count":107,"title":["ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony"],"prefix":"10.1093","volume":"32","author":[{"given":"Edwin","family":"Jacox","sequence":"first","affiliation":[{"name":"1 ISE-M, Universit\u00e9 Montpellier, CNRS, IRD, EPHE, Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cedric","family":"Chauve","sequence":"additional","affiliation":[{"name":"2 Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gergely J.","family":"Sz\u00f6ll\u0151si","sequence":"additional","affiliation":[{"name":"3 ELTE-MTA \u201cLend\u00fclet\u201d Biophysics Research Group, Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yann","family":"Ponty","sequence":"additional","affiliation":[{"name":"4 LIX, CNRS\/Inria AMIB, Ecole Polytechnique, Palaiseau, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Celine","family":"Scornavacca","sequence":"additional","affiliation":[{"name":"1 ISE-M, Universit\u00e9 Montpellier, CNRS, IRD, EPHE, Montpellier, France"},{"name":"5 Institut de Biologie Computationnelle (IBC), Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,2,26]]},"reference":[{"key":"2023020112334801700_btw105-B1","doi-asserted-by":"crossref","first-page":"i283","DOI":"10.1093\/bioinformatics\/bts225","article-title":"Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss","volume":"28","author":"Bansal","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020112334801700_btw105-B2","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1093\/bioinformatics\/btu806","article-title":"Improved gene tree error correction in the presence of horizontal gene transfer","volume":"31","author":"Bansal","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020112334801700_btw105-B3","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1007\/978-1-4471-5298-9_4","volume-title":"Models and Algorithms for Genome Evolution","author":"Chauve","year":"2013"},{"key":"2023020112334801700_btw105-B4","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1093\/bioinformatics\/btv625","article-title":"Sylvx: a viewer for phylogenetic tree reconciliations","volume":"32","author":"Chevenet","year":"2016","journal-title":"Bioinformatics"},{"key":"2023020112334801700_btw105-B5","doi-asserted-by":"crossref","first-page":"16.","DOI":"10.1186\/1748-7188-5-16","article-title":"Jane: a new tool for the cophylogeny reconstruction problem","volume":"5","author":"Conow","year":"2010","journal-title":"Algorithms Mol. 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