{"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":1779896861643,"version":"3.53.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2019,2,1]],"date-time":"2019-02-01T00:00:00Z","timestamp":1548979200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IIS 1553421"],"award-info":[{"award-number":["IIS 1553421"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000152","name":"MCB","doi-asserted-by":"publisher","award":["1616514"],"award-info":[{"award-number":["1616514"]}],"id":[{"id":"10.13039\/100000152","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005246","name":"IES","doi-asserted-by":"publisher","award":["1615573"],"award-info":[{"award-number":["1615573"]}],"id":[{"id":"10.13039\/100005246","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>SaGePhy is a software package for improved phylogenetic simulation of gene and subgene evolution. SaGePhy can be used to generate species trees, gene trees and subgene or (protein) domain trees using a probabilistic birth\u2013death process that allows for gene and subgene duplication, horizontal gene and subgene transfer and gene and subgene loss. SaGePhy implements a range of important features not found in other phylogenetic simulation frameworks\/software. These include (i) simulation of subgene or domain level evolution inside one or more gene trees, (ii) simultaneous simulation of both additive and replacing horizontal gene\/subgene transfers and (iii) probabilistic sampling of species tree and gene tree nodes, respectively, for gene- and domain-family birth. SaGePhy is open-source, platform independent and written in Java and Python.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Executables, source code (open-source under the revised BSD license) and a detailed manual are freely available from http:\/\/compbio.engr.uconn.edu\/software\/sagephy\/.<\/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\/btz081","type":"journal-article","created":{"date-parts":[[2019,2,1]],"date-time":"2019-02-01T04:28:41Z","timestamp":1548995321000},"page":"3496-3498","source":"Crossref","is-referenced-by-count":22,"title":["SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution"],"prefix":"10.1093","volume":"35","author":[{"given":"Soumya","family":"Kundu","sequence":"first","affiliation":[{"name":"Department of Computer Science & Engineering, Storrs , CT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mukul S","family":"Bansal","sequence":"additional","affiliation":[{"name":"Department of Computer Science & Engineering, Storrs , CT, USA"},{"name":"The Institute for Systems Genomics, University of Connecticut, Storrs , CT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,2,1]]},"reference":[{"key":"2023020108350520600_btz081-B1","doi-asserted-by":"crossref","first-page":"283","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":"2023020108350520600_btz081-B2","doi-asserted-by":"crossref","first-page":"3214","DOI":"10.1093\/bioinformatics\/bty314","article-title":"RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss","volume":"34","author":"Bansal","year":"2018","journal-title":"Bioinformatics"},{"key":"2023020108350520600_btz081-B3","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1093\/bioinformatics\/btm024","article-title":"A simulation test bed for hypotheses of genome evolution","volume":"23","author":"Beiko","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020108350520600_btz081-B4","doi-asserted-by":"crossref","first-page":"3309","DOI":"10.1093\/molbev\/mss138","article-title":"Replacing and additive horizontal gene transfer in streptococcus","volume":"29","author":"Choi","year":"2012","journal-title":"Mol. 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