{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T12:48:14Z","timestamp":1762865294069},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: With the increasing amount of DNA sequence data available from natural populations, new computational methods are needed to efficiently process raw sequences into formats that are applicable to a variety of analytical methods. One highly successful approach to inferring aspects of demographic history is grounded in coalescent theory. Many of these methods restrict themselves to perfectly tree-like genealogies (i.e. regions with no observed recombination), because theoretical difficulties prevent ready statistical evaluation of recombining regions. However, determining which recombination-filtered dataset to analyze from a larger recombination-rich genomic region is a non-trivial problem. Current applications primarily aim to quantify recombination rates (rather than produce optimal recombination-filtered blocks), require significant manual intervention, and are impractical for multiple genomic datasets in high-throughput, automated research environments. Here, we present a fast, simple and automatable command-line program that extracts optimal recombination-filtered blocks (no four-gamete violations) from recombination-rich genomic re-sequence data.<\/jats:p><jats:p>Availability: \u00a0http:\/\/hammerlab.biosci.arizona.edu\/software.html<\/jats:p><jats:p>Contact: \u00a0mpcox@email.arizona.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm253","type":"journal-article","created":{"date-parts":[[2007,5,23]],"date-time":"2007-05-23T17:31:07Z","timestamp":1179941467000},"page":"1851-1853","source":"Crossref","is-referenced-by-count":191,"title":["Recombination-filtered genomic datasets by information maximization"],"prefix":"10.1093","volume":"23","author":[{"given":"August E.","family":"Woerner","sequence":"first","affiliation":[{"name":"1 Arizona Research Laboratories \u2013 Biotechnology, University of Arizona, Tucson, AZ 85721 and 2Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA"}]},{"given":"Murray P.","family":"Cox","sequence":"additional","affiliation":[{"name":"1 Arizona Research Laboratories \u2013 Biotechnology, University of Arizona, Tucson, AZ 85721 and 2Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA"},{"name":"1 Arizona Research Laboratories \u2013 Biotechnology, University of Arizona, Tucson, AZ 85721 and 2Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA"}]},{"given":"Michael F.","family":"Hammer","sequence":"additional","affiliation":[{"name":"1 Arizona Research Laboratories \u2013 Biotechnology, University of Arizona, Tucson, AZ 85721 and 2Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA"}]}],"member":"286","published-online":{"date-parts":[[2007,5,22]]},"reference":[{"key":"2023041105233000700_","unstructured":"Drummond AJ \u00a0RambautA BEAST v1.0 2003 http:\/\/beast.bio.ed.ac.uk\/Main_Page"},{"key":"2023041105233000700_","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1093\/genetics\/159.3.1299","article-title":"Estimating recombination rates from population genetic data","volume":"159","author":"Fearnhead","year":"2001","journal-title":"Genetics"},{"key":"2023041105233000700_","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1038\/nrg1941","article-title":"Reconstructing human origins in the genomic era","volume":"7","author":"Garrigan","year":"2006","journal-title":"Nat. Rev. Genet."},{"key":"2023041105233000700_","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/0040-5809(81)90016-2","article-title":"Neutral two-locus multiple allele models with recombination","volume":"19","author":"Griffiths","year":"1981","journal-title":"Theor. Popul. Biol."},{"key":"2023041105233000700_","doi-asserted-by":"crossref","unstructured":"Griffiths RC Genetree v. 9.0 1994 http:\/\/www.stats.ox.ac.uk\/~griff\/software.html","DOI":"10.1049\/sej.1994.0021"},{"key":"2023041105233000700_","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1089\/cmb.1996.3.479","article-title":"Ancestral inference from samples of DNA sequences with recombination","volume":"3","author":"Griffiths","year":"1996","journal-title":"J. Comput. Biol."},{"key":"2023041105233000700_","first-page":"772","article-title":"Archaic African and Asian lineages in the genetic ancestry of modern humans","volume":"60","author":"Harding","year":"1997","journal-title":"Am. J. Hum. Genet."},{"key":"2023041105233000700_","unstructured":"Hey J IM 2005 http:\/\/lifesci.rutgers.edu\/~heylab\/HeylabSoftware.htm#IM"},{"key":"2023041105233000700_","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1534\/genetics.103.024182","article-title":"Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis","volume":"167","author":"Hey","year":"2004","journal-title":"Genetics"},{"key":"2023041105233000700_","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/0040-5809(83)90013-8","article-title":"Properties of a neutral allele model with intragenic recombination","volume":"23","author":"Hudson","year":"1983","journal-title":"Theor. Popul. Biol."},{"key":"2023041105233000700_","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1093\/genetics\/111.1.147","article-title":"Statistical properties of the number of recombination events in the history of a sample of DNA sequences","volume":"111","author":"Hudson","year":"1985","journal-title":"Genetics"},{"key":"2023041105233000700_","doi-asserted-by":"crossref","DOI":"10.2307\/3213548","volume-title":"On the Genealogy of Large Populations","author":"Kingman","year":"1982"},{"key":"2023041105233000700_","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1093\/genetics\/156.3.1393","article-title":"Maximum likelihood estimation of recombination rates from population data","volume":"156","author":"Kuhner","year":"2000","journal-title":"Genetics"},{"key":"2023041105233000700_","unstructured":"McVean G LDhat v.2.0 2004 http:\/\/www.stats.ox.ac.uk\/~mcvean\/LDhat\/"},{"key":"2023041105233000700_","unstructured":"Myers SR RecMin 2003 http:\/\/www.stats.ox.ac.uk\/~myers\/"},{"key":"2023041105233000700_","unstructured":"Sciences National Institute of Environmental Health NIEHS Environmental Genome Project 2007 http:\/\/egp.gs.washington.edu\/"},{"key":"2023041105233000700_","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1093\/oxfordjournals.molbev.a004129","article-title":"Evaluation of methods for detecting recombination from DNA sequences: empirical data","volume":"19","author":"Posada","year":"2002","journal-title":"Mol. Biol. Evol."},{"key":"2023041105233000700_","unstructured":"Stephens M \u00a0LiN PHASE v.2.1 2001 http:\/\/www.stat.washington.edu\/stephens\/software.html"},{"key":"2023041105233000700_","unstructured":"Wilson IJ \u00a0et al. Batwing 2003 http:\/\/www.mas.ncl.ac.uk\/~nijw\/"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/14\/1851\/49814847\/bioinformatics_23_14_1851.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/14\/1851\/49814847\/bioinformatics_23_14_1851.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,11]],"date-time":"2023-05-11T23:24:45Z","timestamp":1683847485000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/14\/1851\/190220"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,5,22]]},"references-count":19,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2007,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm253","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,7,15]]},"published":{"date-parts":[[2007,5,22]]}}}