{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,10,14]],"date-time":"2023-10-14T05:27:46Z","timestamp":1697261266525},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The program COMPASS can generate samples that have been collected at various points in time from a population that is evolving according to a Wright\u2013Fisher model. The samples are generated using coalescence simulations permitting various demographic scenarios and the program uses an infinite sites model to generate polymorphism data for the samples. By generating serially sampled population-genetic data, COMPASS allows investigating properties of polymorphism data that has been collected at different time points, and aid in making inference from ancient polymorphism data.<\/jats:p>\n               <jats:p>Availability: The program and the manual are available at: http:\/\/www.egs.uu.se\/evbiol\/Research\/JakobssonLab\/compass.html<\/jats:p>\n               <jats:p>Contact: \u00a0mattias.jakobsson@ebc.uu.se<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp534","type":"journal-article","created":{"date-parts":[[2009,9,18]],"date-time":"2009-09-18T03:59:51Z","timestamp":1253246391000},"page":"2845-2847","source":"Crossref","is-referenced-by-count":9,"title":["<i>COMPASS<\/i>: a program for generating serial samples under an infinite sites model"],"prefix":"10.1093","volume":"25","author":[{"given":"Mattias","family":"Jakobsson","sequence":"first","affiliation":[{"name":"Department of Evolutionary Biology, Uppsala University, Norbyv\u00e4gen 18D, 75236 Uppsala, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2009,9,17]]},"reference":[{"key":"2023013112185352100_B1","doi-asserted-by":"crossref","first-page":"1733","DOI":"10.1093\/bioinformatics\/bti154","article-title":"Serial SimCoal: a population genetics model for data from multiple populations and points in time","volume":"21","author":"Anderson","year":"2005","journal-title":"Bioinformatics"},{"key":"2023013112185352100_B2","doi-asserted-by":"crossref","first-page":"2025","DOI":"10.1093\/genetics\/162.4.2025","article-title":"Approximate Bayesian computation in population genetics","volume":"162","author":"Beaumont","year":"2002","journal-title":"Genetics"},{"key":"2023013112185352100_B3","doi-asserted-by":"crossref","first-page":"3736","DOI":"10.1073\/pnas.0607187104","article-title":"Absence of the lactase-persistence-associated allele in early Neolithic Europeans","volume":"104","author":"Burger","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013112185352100_B4","doi-asserted-by":"crossref","first-page":"e5541","DOI":"10.1371\/journal.pone.0005541","article-title":"Using classical population genetics tools with heterochroneous data: time matters!","volume":"4","author":"Depaulis","year":"2009","journal-title":"PLoS ONE"},{"key":"2023013112185352100_B5","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1093\/genetics\/161.3.1307","article-title":"Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data","volume":"161","author":"Drummond","year":"2002","journal-title":"Genetics"},{"key":"2023013112185352100_B6","doi-asserted-by":"crossref","first-page":"2586","DOI":"10.1016\/j.quascirev.2008.09.012","article-title":"Long DNA sequences and large data sets: investigating the quaternary via ancient dna","volume":"27","author":"Hofreiter","year":"2008","journal-title":"Quat. Sci. Rev."},{"key":"2023013112185352100_B7","first-page":"1","article-title":"Gene genealogies and the coalescent process","volume":"7","author":"Hudson","year":"1990","journal-title":"Oxford Surv. Evol. Biol."},{"key":"2023013112185352100_B8","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":"2023013112185352100_B9","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1093\/genetics\/61.4.893","article-title":"The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations","volume":"61","author":"Kimura","year":"1969","journal-title":"Genetics"},{"key":"2023013112185352100_B10","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1017\/S0021900200034446","article-title":"On the genealogy of large populations","volume":"19A","author":"Kingman","year":"1982","journal-title":"J. Appl. Prob."},{"key":"2023013112185352100_B11","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1126\/science.1172750","article-title":"Coat color variation at the beginning of horse domestication","volume":"324","author":"Ludwig","year":"2009","journal-title":"Science"},{"key":"2023013112185352100_B12","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1038\/nature07446","article-title":"Sequencing the nuclear genome of the extinct woolly mammoth","volume":"456","author":"Miller","year":"2008","journal-title":"Nature"},{"key":"2023013112185352100_B13","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1126\/science.1113485","article-title":"Paleontology: Genomic sequencing of pleistocene cave bears","volume":"309","author":"Noonan","year":"2005","journal-title":"Science"},{"key":"2023013112185352100_B14","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1126\/science.1131412","article-title":"Sequencing and analysis of Neanderthal genomic DNA","volume":"314","author":"Noonan","year":"2006","journal-title":"Science"},{"key":"2023013112185352100_B15","first-page":"179","article-title":"Coalescent theory, Ch. 7","volume-title":"Handbook of Statistical Genetics","author":"Nordborg","year":"2001"},{"key":"2023013112185352100_B16","first-page":"235","article-title":"Seq-gen: An application for the monte carlo simulation of dna sequence evolution along phylogenetic trees","volume":"13","author":"Rambaut","year":"1997","journal-title":"Comput. Appli. Biosci."},{"key":"2023013112185352100_B17","doi-asserted-by":"crossref","first-page":"6785","DOI":"10.1073\/pnas.100140097","article-title":"Characterization of the 1918 \u201cSpanish\u201d influenza virus neuraminidase gene","volume":"97","author":"Reid","year":"2000","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013112185352100_B18","first-page":"233","article-title":"Coalescent approaches to HIV population genetics","volume-title":"The Evolution of HIV.","author":"Rodrigo","year":"1999"},{"key":"2023013112185352100_B19","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1111\/j.1365-2052.2007.01620.x","article-title":"Tracing genetic change over time using nuclear SNPs in ancient and modern cattle","volume":"38","author":"Svensson","year":"2007","journal-title":"Animal Genet."},{"key":"2023013112185352100_B20","volume-title":"Genetic Data Analysis II.","author":"Weir","year":"1996"},{"key":"2023013112185352100_B21","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1098\/rspb.2004.2813","article-title":"Ancient dna","volume":"272","author":"Willerslev","year":"2005","journal-title":"Proc. R. Soc. B Biol. Sci."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/21\/2845\/48997583\/bioinformatics_25_21_2845.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/21\/2845\/48997583\/bioinformatics_25_21_2845.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T21:58:08Z","timestamp":1675202288000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/21\/2845\/228700"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,9,17]]},"references-count":21,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2009,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp534","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,11,1]]},"published":{"date-parts":[[2009,9,17]]}}}