{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:19Z","timestamp":1740185119921,"version":"3.37.3"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"17","funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["0906018"],"award-info":[{"award-number":["0906018"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Most population genetic simulators fall into one of two classes, backward time simulators that quickly generate trees but accommodate only relatively simple selective and demographic regimes, and forward simulators that allow for a broader range of evolutionary scenarios but which cannot produce genealogies. Thus, few tools are available that allow for producing genealogies under arbitrarily complex selective and demographic models.<\/jats:p>\n               <jats:p>Results: TreesimJ is a forward time population genetic simulator that allows for sampling of genealogies, genetic data and many population parameters from populations evolving under complex evolutionary scenarios. The application provides many fitness and demographic models and new models are easy to develop. Data collection is performed by a variety of independently configurable collectors which periodically sample the population and record statistics. Output options include writing traces, histograms and summary statistics from the data collectors in addition to sampled genetic sequences and genealogies.<\/jats:p>\n               <jats:p>Summary: TreesimJ allows researchers to easily sample and analyze gene genealogies and related data from populations evolving under a wide variety of selective and demographic regimes. It is likely to be useful for population genetic researchers seeking to understand the links between evolutionary and demographic forces, genealogical structure and the resulting patterns of genetic variation.<\/jats:p>\n               <jats:p>Availability: TreesimJ home : http:\/\/staff.washington.edu\/brendano\/treesimj. Source and developer resources: http:\/\/code.google.com\/p\/treesimj<\/jats:p>\n               <jats:p>Contact: \u00a0brendano@u.washington.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq355","type":"journal-article","created":{"date-parts":[[2010,7,30]],"date-time":"2010-07-30T02:42:33Z","timestamp":1280457753000},"page":"2200-2201","source":"Crossref","is-referenced-by-count":14,"title":["TreesimJ: a flexible, forward time population genetic\n          simulator"],"prefix":"10.1093","volume":"26","author":[{"given":"Brendan","family":"O'Fallon","sequence":"first","affiliation":[{"name":"Department of Genome Sciences, Foege Building S-250, Box 355065 3720 15th Ave NE, Seattle WA 98195-5065, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,7,29]]},"reference":[{"key":"2023012508014384300_B1","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1093\/jhered\/92.3.301","article-title":"EASYPOP (version 1.7): a computer program for population genetics\n            simulations","volume":"92","author":"Balloux","year":"2001","journal-title":"J. Hered."},{"key":"2023012508014384300_B2","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1186\/1471-2105-9-223","article-title":"GENOMEPOP: a program to simulate genomes in populations","volume":"9","author":"Carvajal-Rodriguez","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012508014384300_B3","doi-asserted-by":"crossref","first-page":"2556","DOI":"10.1093\/bioinformatics\/btl415","article-title":"Nemo: an evolutionary and population genetics programming\n            framework","volume":"22","author":"Guillaume","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012508014384300_B4","doi-asserted-by":"crossref","first-page":"2786","DOI":"10.1093\/bioinformatics\/btn522","article-title":"A flexible forward simulator for populations subject to selection and\n            demography","volume":"24","author":"Hernandez","year":"2008","journal-title":"Bioinformatics"},{"journal-title":"FPG: a computer program for forward population genetics simulation.","year":"2004","author":"Hey","key":"2023012508014384300_B5"},{"key":"2023012508014384300_B6","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1093\/bioinformatics\/18.2.337","article-title":"Generating samples under a Wright-Fisher neutral model","volume":"18","author":"Hudson","year":"2002","journal-title":"Bioinformatics"},{"key":"2023012508014384300_B7","doi-asserted-by":"crossref","first-page":"2485","DOI":"10.1093\/bioinformatics\/bth264","article-title":"SimCoal 2: a program to simulate genomic diversity over large recombining\n            regions in a subdivided population with a complex history","volume":"20","author":"Laval","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012508014384300_B8","doi-asserted-by":"crossref","first-page":"3673","DOI":"10.1093\/bioinformatics\/bth417","article-title":"SelSim: a program to simulate population genetic data with natural\n            selection and recombination","volume":"20","author":"Spencer","year":"2004","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/17\/2200\/48854907\/bioinformatics_26_17_2200.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/17\/2200\/48854907\/bioinformatics_26_17_2200.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:01:56Z","timestamp":1674633716000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/17\/2200\/199321"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,7,29]]},"references-count":8,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2010,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq355","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"type":"electronic","value":"1367-4811"},{"type":"print","value":"1367-4803"}],"subject":[],"published-other":{"date-parts":[[2010,9,1]]},"published":{"date-parts":[[2010,7,29]]}}}