{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T21:31:54Z","timestamp":1778880714822,"version":"3.51.4"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2020,7,16]],"date-time":"2020-07-16T00:00:00Z","timestamp":1594857600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Gene and species tree reconciliation methods are used to interpret gene trees, root them and correct uncertainties that are due to scarcity of signal in multiple sequence alignments. So far, reconciliation tools have not been integrated in standard phylogenetic software and they either lack performance on certain functions, or usability for biologists.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present Treerecs, a phylogenetic software based on duplication-loss reconciliation. Treerecs is simple to install and to use. It is fast and versatile, has a graphic output, and can be used along with methods for phylogenetic inference on multiple alignments like PLL and Seaview.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Treerecs is open-source. Its source code (C++, AGPLv3) and manuals are available from https:\/\/project.inria.fr\/treerecs\/.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa615","type":"journal-article","created":{"date-parts":[[2020,7,10]],"date-time":"2020-07-10T07:34:24Z","timestamp":1594366464000},"page":"4822-4824","source":"Crossref","is-referenced-by-count":39,"title":["Treerecs: an integrated phylogenetic tool, from sequences to reconciliations"],"prefix":"10.1093","volume":"36","author":[{"given":"Nicolas","family":"Comte","sequence":"first","affiliation":[{"name":"Inria Grenoble Rh\u00f4ne-Alpes , 38334 Montbonnot, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benoit","family":"Morel","sequence":"additional","affiliation":[{"name":"Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Damir","family":"Hasi\u0107","sequence":"additional","affiliation":[{"name":"Department of Mathematics, University of Sarajevo, Sarajevo, Bosnia and Herzegovina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laurent","family":"Gu\u00e9guen","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Lyon, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive , CNRS UMR5558, F-69622 Villeurbanne, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bastien","family":"Boussau","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Lyon, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive , CNRS UMR5558, F-69622 Villeurbanne, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vincent","family":"Daubin","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Lyon, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive , CNRS UMR5558, F-69622 Villeurbanne, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simon","family":"Penel","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Lyon, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive , CNRS UMR5558, F-69622 Villeurbanne, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Celine","family":"Scornavacca","sequence":"additional","affiliation":[{"name":"ISEM, CNRS, Universit\u00e9 de Montpellier, IRD, EPHE, Montpellier 34000, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manolo","family":"Gouy","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Lyon, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive , CNRS UMR5558, F-69622 Villeurbanne, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexandros","family":"Stamatakis","sequence":"additional","affiliation":[{"name":"Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany"},{"name":"Institute of Theoretical Informatics, Karlsruhe Institute of Technology , Karlsruhe, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Tannier","sequence":"additional","affiliation":[{"name":"Inria Grenoble Rh\u00f4ne-Alpes , 38334 Montbonnot, France"},{"name":"Universit\u00e9 de Lyon, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive , CNRS UMR5558, F-69622 Villeurbanne, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0511-0703","authenticated-orcid":false,"given":"David P","family":"Parsons","sequence":"additional","affiliation":[{"name":"Inria Grenoble Rh\u00f4ne-Alpes , 38334 Montbonnot, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,7,16]]},"reference":[{"key":"2023062213564991500_btaa615-B1","doi-asserted-by":"crossref","first-page":"5714","DOI":"10.1073\/pnas.0806251106","article-title":"Simultaneous Bayesian gene tree reconstruction and reconciliation analysis","volume":"106","author":"Akerborg","year":"2009","journal-title":"Proc. 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