{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,12]],"date-time":"2026-07-12T01:40:42Z","timestamp":1783820442950,"version":"3.55.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2018,8,23]],"date-time":"2018-08-23T00:00:00Z","timestamp":1534982400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["31003A_138180"],"award-info":[{"award-number":["31003A_138180"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>QuantiNemo 2 is a stochastic simulation program for quantitative population genetics. It was developed to investigate the effects of selection, mutation, recombination and drift on quantitative traits and neutral markers in structured populations connected by migration and located in heterogeneous habitats. A specific feature is that it allows to switch between an individual-based full-featured mode and a population-based faster mode. Several demographic, genetic and selective parameters can be fine-tuned in QuantiNemo 2: population, selection, trait(s) architecture, genetic map for QTL and\/or markers, environment, demography and mating system are the main features.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>QuantiNemo 2 is a C++ program with a source code available under the GNU General Public License version 3. Executables are provided for Windows, MacOS and Linux platforms, together with a comprehensive manual and tutorials illustrating its flexibility. The executable, manual and tutorial can be found on the website www2.unil.ch\/popgen\/softwares\/quantinemo\/, while the source code and user support are given through GitHub: github.com\/jgx65\/quantinemo.<\/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\/bty737","type":"journal-article","created":{"date-parts":[[2018,8,22]],"date-time":"2018-08-22T19:19:20Z","timestamp":1534965560000},"page":"886-888","source":"Crossref","is-referenced-by-count":31,"title":["QuantiNemo 2: a Swiss knife to simulate complex demographic and genetic scenarios, forward and backward in time"],"prefix":"10.1093","volume":"35","author":[{"given":"Samuel","family":"Neuenschwander","sequence":"first","affiliation":[{"name":"Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland"},{"name":"Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fr\u00e9d\u00e9ric","family":"Michaud","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland"},{"name":"Swiss Institute of Bioinformatics, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00e9r\u00f4me","family":"Goudet","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland"},{"name":"Swiss Institute of Bioinformatics, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,8,23]]},"reference":[{"key":"2023013107255709700_bty737-B1","doi-asserted-by":"crossref","first-page":"5508","DOI":"10.1111\/mec.12957","article-title":"Natural selection in a postglacial range expansion: the case of the colour cline in the European barn owl","volume":"23","author":"Antoniazza","year":"2014","journal-title":"Mol. Ecol"},{"key":"2023013107255709700_bty737-B2","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1111\/jeb.13235","article-title":"Sex-antagonistic genes, xy recombination and feminized y chromosomes","volume":"31","author":"Cavoto","year":"2018","journal-title":"J. Evol. Biol"},{"key":"2023013107255709700_bty737-B3","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1111\/j.1755-0998.2010.02847.x","article-title":"Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under linux and windows","volume":"10","author":"Excoffier","year":"2010","journal-title":"Mol. Ecol. Res"},{"key":"2023013107255709700_bty737-B4","doi-asserted-by":"crossref","first-page":"e1003905","DOI":"10.1371\/journal.pgen.1003905","article-title":"Robust demographic inference from genomic and SNP data","volume":"9","author":"Excoffier","year":"2013","journal-title":"PLoS Genet"},{"key":"2023013107255709700_bty737-B5","doi-asserted-by":"crossref","first-page":"2556","DOI":"10.1093\/bioinformatics\/btl415","article-title":"Nemo: an evolutionary and population genetics programming framework","volume":"22","author":"Guillaume","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013107255709700_bty737-B6","doi-asserted-by":"crossref","first-page":"110\u2013122","DOI":"10.1038\/nrg3130","article-title":"Computer simulations: tools for population and evolutionary genetics","volume":"13","author":"Hoban","year":"2012","journal-title":"Nat. Rev. Genet"},{"key":"2023013107255709700_bty737-B7","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1093\/bioinformatics\/18.2.337","article-title":"Generating samples under a wright-fisher neutral model of genetic variation","volume":"18","author":"Hudson","year":"2002","journal-title":"Bioinformatics"},{"key":"2023013107255709700_bty737-B8","doi-asserted-by":"crossref","first-page":"e0192460","DOI":"10.1371\/journal.pone.0192460","article-title":"Complex genetic patterns in human arise from a simple range-expansion model over continental landmasses","volume":"13","author":"Kanitz","year":"2018","journal-title":"PLoS One"},{"key":"2023013107255709700_bty737-B9","doi-asserted-by":"crossref","first-page":"1552","DOI":"10.1093\/bioinformatics\/btn219","article-title":"quantinemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation","volume":"24","author":"Neuenschwander","year":"2008","journal-title":"Bioinformatics"},{"key":"2023013107255709700_bty737-B10","doi-asserted-by":"crossref","first-page":"3686","DOI":"10.1093\/bioinformatics\/bti584","article-title":"simupop: a forward-time population genetics simulation environment","volume":"21","author":"Peng","year":"2005","journal-title":"Bioinformatics"},{"key":"2023013107255709700_bty737-B11","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1093\/bioinformatics\/btt094","article-title":"Genetic simulation resources: a website for the registration and discovery of genetic data simulators","volume":"29","author":"Peng","year":"2013","journal-title":"Bioinformatics"},{"key":"2023013107255709700_bty737-B12","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"Plink: a tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. Genet"},{"key":"2023013107255709700_bty737-B13","doi-asserted-by":"crossref","first-page":"2993","DOI":"10.1093\/bioinformatics\/btq579","article-title":"SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination","volume":"26","author":"Ray","year":"2010","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/5\/886\/48966101\/bioinformatics_35_5_886.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/5\/886\/48966101\/bioinformatics_35_5_886.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T10:21:41Z","timestamp":1675160501000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/5\/886\/5078477"}},"subtitle":[],"editor":[{"given":"Oliver","family":"Stegle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,8,23]]},"references-count":13,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2019,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty737","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,3,1]]},"published":{"date-parts":[[2018,8,23]]}}}