{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T20:17:50Z","timestamp":1774469870851,"version":"3.50.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2018,4,24]],"date-time":"2018-04-24T00:00:00Z","timestamp":1524528000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"U.S. National Science Foundation","doi-asserted-by":"crossref","award":["1553421"],"award-info":[{"award-number":["1553421"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000001","name":"U.S. National Science Foundation","doi-asserted-by":"crossref","award":["1616514"],"award-info":[{"award-number":["1616514"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000001","name":"U.S. National Science Foundation","doi-asserted-by":"crossref","award":["1615573"],"award-info":[{"award-number":["1615573"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"crossref"}]},{"name":"University of Connecticut Summer Undergraduate Research Fund award"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>RANGER-DTL 2.0 is a software program for inferring gene family evolution using Duplication-Transfer-Loss reconciliation. This new software is highly scalable and easy to use, and offers many new features not currently available in any other reconciliation program. RANGER-DTL 2.0 has a particular focus on reconciliation accuracy and can account for many sources of reconciliation uncertainty including uncertain gene tree rooting, gene tree topological uncertainty, multiple optimal reconciliations and alternative event cost assignments. RANGER-DTL 2.0 is open-source and written in C++\u2009and Python.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Pre-compiled executables, source code (open-source under GNU GPL) and a detailed manual are freely available from http:\/\/compbio.engr.uconn.edu\/software\/RANGER-DTL\/.<\/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\/bty314","type":"journal-article","created":{"date-parts":[[2018,4,20]],"date-time":"2018-04-20T19:10:23Z","timestamp":1524251423000},"page":"3214-3216","source":"Crossref","is-referenced-by-count":101,"title":["RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss"],"prefix":"10.1093","volume":"34","author":[{"given":"Mukul S","family":"Bansal","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA"}]},{"given":"Manolis","family":"Kellis","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA"},{"name":"Broad Institute, Cambridge, MA, USA"}]},{"given":"Misagh","family":"Kordi","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA"}]},{"given":"Soumya","family":"Kundu","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,4,24]]},"reference":[{"key":"2023012704180379900_bty314-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":"2023012704180379900_bty314-B2","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1089\/cmb.2013.0073","article-title":"Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss","volume":"20","author":"Bansal","year":"2013","journal-title":"J. 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