{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T02:26:47Z","timestamp":1782959207453,"version":"3.54.5"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,9,30]],"date-time":"2019-09-30T00:00:00Z","timestamp":1569801600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Research Council under the European Union\u2019s Horizon 2020","award":["GINOP-2.3.2.-15-2016-00057"],"award-info":[{"award-number":["GINOP-2.3.2.-15-2016-00057"]}]},{"name":"European Research Council under the European Union\u2019s Horizon 2020","award":["ANR-18-CE02-0007-01"],"award-info":[{"award-number":["ANR-18-CE02-0007-01"]}]}],"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>Summary<\/jats:title>\n                    <jats:p>Here we present Zombi, a tool to simulate the evolution of species, genomes and sequences in silico, that considers for the first time the evolution of genomes in extinct lineages. It also incorporates various features that have not to date been combined in a single simulator, such as the possibility of generating species trees with a pre-defined variation of speciation and extinction rates through time, simulating explicitly intergenic sequences of variable length and outputting gene tree\u2014species tree reconciliations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Source code and manual are freely available in https:\/\/github.com\/AADavin\/ZOMBI\/.<\/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\/btz710","type":"journal-article","created":{"date-parts":[[2019,9,26]],"date-time":"2019-09-26T07:28:48Z","timestamp":1569482928000},"page":"1286-1288","source":"Crossref","is-referenced-by-count":35,"title":["Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages"],"prefix":"10.1093","volume":"36","author":[{"given":"Adri\u00e1n A","family":"Dav\u00edn","sequence":"first","affiliation":[{"name":"MTA-ELTE Lend\u00fclet Evolutionary Genomics Research Group , Budapest, Hungary"},{"name":"Department of Biological Physics, E\u00f6tv\u00f6s Lor\u00e1nd , Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Th\u00e9o","family":"Tricou","sequence":"additional","affiliation":[{"name":"Univ Lyon, Universit\u00e9 Lyon 1, CNRS, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive UMR5558 , Villeurbanne F-69622, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Tannier","sequence":"additional","affiliation":[{"name":"Univ Lyon, Universit\u00e9 Lyon 1, CNRS, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive UMR5558 , Villeurbanne F-69622, France"},{"name":"INRIA Grenoble Rh\u00f4ne-Alpes , Montbonnot-Saint-Martin F-38334, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Damien M","family":"de Vienne","sequence":"additional","affiliation":[{"name":"Univ Lyon, Universit\u00e9 Lyon 1, CNRS, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive UMR5558 , Villeurbanne F-69622, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gergely J","family":"Sz\u00f6ll\u0151si","sequence":"additional","affiliation":[{"name":"MTA-ELTE Lend\u00fclet Evolutionary Genomics Research Group , Budapest, Hungary"},{"name":"Department of Biological Physics, E\u00f6tv\u00f6s Lor\u00e1nd , Budapest, Hungary"},{"name":"Evolutionary Systems Research Group , Centre for Ecological Research, Hungarian Academy of Sciences, Tihany H-8237, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,9,30]]},"reference":[{"key":"2023013110150605800_btz710-B1","doi-asserted-by":"crossref","first-page":"4962","DOI":"10.1073\/pnas.1116871109","article-title":"Lateral gene transfer as a support for the tree of life","volume":"109","author":"Abby","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023013110150605800_btz710-B2","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":"2023013110150605800_btz710-B3","doi-asserted-by":"crossref","first-page":"1427","DOI":"10.1093\/gbe\/evw083","article-title":"Breaking good: accounting for fragility of genomic regions in rearrangement distance estimation","volume":"8","author":"Biller","year":"2016","journal-title":"Genome Biol. Evol"},{"key":"2023013110150605800_btz710-B4","doi-asserted-by":"crossref","first-page":"272.","DOI":"10.1186\/1471-2148-8-272","article-title":"Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of bacteria","volume":"8","author":"Boussau","year":"2008","journal-title":"BMC Evol. Biol"},{"key":"2023013110150605800_btz710-B5","doi-asserted-by":"crossref","first-page":"155","DOI":"10.2174\/138920208784340759","article-title":"Simulation of genomes: a review","volume":"9","author":"Carvajal-Rodr\u00edguez","year":"2008","journal-title":"Curr. Genomics"},{"key":"2023013110150605800_btz710-B6","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1093\/molbev\/msr268","article-title":"ALF\u2014a simulation framework for genome evolution","volume":"29","author":"Dalquen","year":"2012","journal-title":"Mol. Biol. Evol"},{"key":"2023013110150605800_btz710-B7","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1038\/s41559-018-0525-3","article-title":"Gene transfers can date the tree of life","volume":"2","author":"Dav\u00edn","year":"2018","journal-title":"Nat. Ecol. Evol"},{"key":"2023013110150605800_btz710-B8","doi-asserted-by":"crossref","first-page":"3646","DOI":"10.1093\/bioinformatics\/bty389","article-title":"RecPhyloXML \u2013 a format for reconciled gene trees","volume":"34","author":"Duchemin","year":"2018","journal-title":"Bioinformatics"},{"key":"2023013110150605800_btz710-B9","doi-asserted-by":"crossref","first-page":"2229","DOI":"10.1098\/rstb.2009.0033","article-title":"Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life","volume":"364","author":"Fournier","year":"2009","journal-title":"Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci"},{"key":"2023013110150605800_btz710-B10","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1021\/j100540a008","article-title":"Exact stochastic simulation of coupled chemical reactions","volume":"81","author":"Gillespie","year":"1977","journal-title":"J. Phys. Chem"},{"key":"2023013110150605800_btz710-B11","doi-asserted-by":"crossref","first-page":"465.","DOI":"10.1093\/sysbio\/syq026","article-title":"Sampling trees from evolutionary models","volume":"59","author":"Hartmann","year":"2010","journal-title":"Syst. Biol"},{"key":"2023013110150605800_btz710-B12","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1093\/molbev\/msw046","article-title":"ETE 3: reconstruction, analysis, and visualization of phylogenomic data","volume":"33","author":"Huerta-Cepas","year":"2016","journal-title":"Mol. Biol. Evol"},{"key":"2023013110150605800_btz710-B13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1214\/aoms\/1177730285","article-title":"On the generalized \u2018Birth-and-Death\u2019 process","volume":"19","author":"Kendall","year":"1948","journal-title":"Ann. Math. Stat"},{"key":"2023013110150605800_btz710-B14","doi-asserted-by":"crossref","first-page":"3496","DOI":"10.1093\/bioinformatics\/btz081","article-title":"SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution","volume":"35","author":"Kundu","year":"2019","journal-title":"Bioinformatics"},{"key":"2023013110150605800_btz710-B15","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1139\/cjm-2018-0275","article-title":"Horizontal transfer of antibiotic resistance genes in clinical environments","volume":"65","author":"Lerminiaux","year":"2019","journal-title":"Can. J. Microbiol"},{"key":"2023013110150605800_btz710-B16","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1093\/sysbio\/syv082","article-title":"SimPhy: phylogenomic simulation of gene, locus, and species trees","volume":"65","author":"Mallo","year":"2016","journal-title":"Syst. Biol"},{"key":"2023013110150605800_btz710-B17","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1038\/35012500","article-title":"Lateral gene transfer and the nature of bacterial innovation","volume":"405","author":"Ochman","year":"2000","journal-title":"Nature"},{"key":"2023013110150605800_btz710-B18","article-title":"Power-law distribution from exponential processes: an explanation for the occurrence of long-tailed distributions in biology and elsewhere","author":"Reed","year":"2003","journal-title":"Sci. Math. Jpn"},{"key":"2023013110150605800_btz710-B19","doi-asserted-by":"crossref","first-page":"209.","DOI":"10.1186\/1471-2105-14-209","article-title":"GenPhyloData: realistic simulation of gene family evolution","volume":"14","author":"Sj\u00f6strand","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023013110150605800_btz710-B20","doi-asserted-by":"crossref","first-page":"e0139047.","DOI":"10.1371\/journal.pone.0139047","article-title":"Pyvolve: a flexible python module for simulating sequences along phylogenies","volume":"10","author":"Spielman","year":"2015","journal-title":"PLoS One"},{"key":"2023013110150605800_btz710-B26","article-title":"The pattern and process of gene family evolution","author":"Sz\u00f6ll\u0151si","year":"2011","journal-title":"arXiv preprint arXiv:1102.2331"},{"key":"2023013110150605800_btz710-B21","doi-asserted-by":"crossref","first-page":"17513","DOI":"10.1073\/pnas.1202997109","article-title":"Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations","volume":"109","author":"Sz\u00f6ll\u0151si","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023013110150605800_btz710-B22","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1093\/sysbio\/syt003","article-title":"Lateral gene transfer from the dead","volume":"62","author":"Sz\u00f6ll\u0151si","year":"2013","journal-title":"Syst. Biol"},{"key":"2023013110150605800_btz710-B23","doi-asserted-by":"crossref","first-page":"E4602","DOI":"10.1073\/pnas.1618463114","article-title":"Integrative modeling of gene and genome evolution roots the archaeal tree of life","volume":"114","author":"Williams","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023013110150605800_btz710-B24","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1038\/s41559-018-0513-7","article-title":"Horizontal gene transfer constrains the timing of methanogen evolution","volume":"2","author":"Wolfe","year":"2018","journal-title":"Nat. Ecol. Evol"},{"key":"2023013110150605800_btz710-B25","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1016\/j.tig.2004.02.004","article-title":"Cladogenesis, coalescence and the evolution of the three domains of life","volume":"20","author":"Zhaxybayeva","year":"2004","journal-title":"Trends Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz710\/31084319\/btz710.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/4\/1286\/48983579\/bioinformatics_36_4_1286.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/4\/1286\/48983579\/bioinformatics_36_4_1286.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T15:16:38Z","timestamp":1675178198000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/4\/1286\/5578480"}},"subtitle":[],"editor":[{"given":"Russell","family":"Schwartz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,9,30]]},"references-count":26,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2020,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz710","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/339473","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,2,15]]},"published":{"date-parts":[[2019,9,30]]}}}