{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,24]],"date-time":"2025-03-24T08:18:00Z","timestamp":1742804280398,"version":"3.37.3"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,10,4]],"date-time":"2019-10-04T00:00:00Z","timestamp":1570147200000},"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\/100008725","name":"Agencia Nacional de Investigaci\u00f3n e Innovaci\u00f3n","doi-asserted-by":"crossref","award":["POS_NAC_2018_1_151494"],"award-info":[{"award-number":["POS_NAC_2018_1_151494"]}],"id":[{"id":"10.13039\/100008725","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The pangenome concept describes genetic variability as the union of genes shared in a set of genomes and constitutes the current paradigm for comparative analysis of bacterial populations. However, there is a lack of tools to simulate pangenome variability and structure using defined evolutionary models.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed simurg, an R package that allows to simulate bacterial pangenomes using different combinations of evolutionary constraints such as gene gain, gene loss and mutation rates. Our tool allows the straightforward and reproducible simulation of bacterial pangenomes using real sequence data, providing a valuable tool for benchmarking of pangenome software or comparing evolutionary hypotheses.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The simurg package is released under the GPL-3 license, and is freely available for download from GitHub (https:\/\/github.com\/iferres\/simurg).<\/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\/btz735","type":"journal-article","created":{"date-parts":[[2019,9,26]],"date-time":"2019-09-26T11:28:48Z","timestamp":1569497328000},"page":"1273-1274","source":"Crossref","is-referenced-by-count":5,"title":["simurg: simulate bacterial pangenomes in R"],"prefix":"10.1093","volume":"36","author":[{"given":"Ignacio","family":"Ferr\u00e9s","sequence":"first","affiliation":[{"name":"Microbial Genomics Laboratory, Institut Pasteur Montevideo , Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pablo","family":"Fresia","sequence":"additional","affiliation":[{"name":"Microbial Genomics Laboratory, Institut Pasteur Montevideo , Uruguay"},{"name":"Unidad Mixta UMPI, Institut Pasteur Montevideo + INIA , Montevideo 11400, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gregorio","family":"Iraola","sequence":"additional","affiliation":[{"name":"Microbial Genomics Laboratory, Institut Pasteur Montevideo , Uruguay"},{"name":"Center for Integrative Biology, Universidad Mayor , Santiago de Chile 7510041, Chile"},{"name":"Wellcome Sanger Institute , Hinxton CB10 1SA, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,10,4]]},"reference":[{"key":"2023013110153390600_btz735-B1","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1038\/s41437-017-0034-1","article-title":"Coalescent framework for prokaryotes undergoing interspecific homologous recombination","volume":"120","author":"Akita","year":"2018","journal-title":"Heredity"},{"key":"2023013110153390600_btz735-B2","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1093\/gbe\/evs016","article-title":"The infinitely many genes model for the distributed genome of bacteria","volume":"4","author":"Baumdicker","year":"2012","journal-title":"Genome Biol. 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