{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T10:11:29Z","timestamp":1776075089429,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2016,12,29]],"date-time":"2016-12-29T00:00:00Z","timestamp":1482969600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100006221","name":"U.S. National Science Foundation","doi-asserted-by":"publisher","award":["IIS-0953563 and IIS-1447711"],"award-info":[{"award-number":["IIS-0953563 and IIS-1447711"]}],"id":[{"id":"10.13039\/100006221","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006221","name":"U.S. National Science Foundation","doi-asserted-by":"publisher","award":["S10-RR027140"],"award-info":[{"award-number":["S10-RR027140"]}],"id":[{"id":"10.13039\/100006221","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Haplotypes from one or multiple related populations share a common genealogical history. If this shared genealogy can be inferred from haplotypes, it can be very useful for many population genetics problems. However, with the presence of recombination, the genealogical history of haplotypes is complex and cannot be represented by a single genealogical tree. Therefore, inference of genealogical history with recombination is much more challenging than the case of no recombination.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this paper, we present a new approach called RENT+\u2009for the inference of local genealogical trees from haplotypes with the presence of recombination. RENT+\u2009builds on a previous genealogy inference approach called RENT, which infers a set of related genealogical trees at different genomic positions. RENT+\u2009represents a significant improvement over RENT in the sense that it is more effective in extracting information contained in the haplotype data about the underlying genealogy than RENT. The key components of RENT+\u2009are several greatly enhanced genealogy inference rules. Through simulation, we show that RENT+\u2009is more efficient and accurate than several existing genealogy inference methods. As an application, we apply RENT+\u2009in the inference of population demographic history from haplotypes, which outperforms several existing methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>RENT+\u2009is implemented in Java, and is freely available for download from: https:\/\/github.com\/SajadMirzaei\/RentPlus.<\/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\/btw735","type":"journal-article","created":{"date-parts":[[2016,11,17]],"date-time":"2016-11-17T04:08:19Z","timestamp":1479355699000},"page":"1021-1030","source":"Crossref","is-referenced-by-count":33,"title":["RENT+: an improved method for inferring local genealogical trees from haplotypes with recombination"],"prefix":"10.1093","volume":"33","author":[{"given":"Sajad","family":"Mirzaei","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA"}]},{"given":"Yufeng","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,12,29]]},"reference":[{"key":"2023020204524297100_btw735-B1","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.jtbi.2015.03.006","article-title":"Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites","volume":"374","author":"Chifman","year":"2015","journal-title":"J. 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