{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T20:05:31Z","timestamp":1774382731596,"version":"3.50.1"},"reference-count":85,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2021,6,4]],"date-time":"2021-06-04T00:00:00Z","timestamp":1622764800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100020628","name":"Information and Communication Technology Division","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100020628","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Government of the People\u2019s Republic of Bangladesh"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Species tree estimation from genes sampled from throughout the whole genome is complicated due to the gene tree\u2013species tree discordance. Incomplete lineage sorting (ILS) is one of the most frequent causes for this discordance, where alleles can coexist in populations for periods that may span several speciation events. Quartet-based summary methods for estimating species trees from a collection of gene trees are becoming popular due to their high accuracy and statistical guarantee under ILS. Generating quartets with appropriate weights, where weights correspond to the relative importance of quartets, and subsequently amalgamating the weighted quartets to infer a single coherent species tree can allow for a statistically consistent way of estimating species trees. However, handling weighted quartets is challenging.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose wQFM, a highly accurate method for species tree estimation from multi-locus data, by extending the quartet FM (QFM) algorithm to a weighted setting. wQFM was assessed on a collection of simulated and real biological datasets, including the avian phylogenomic dataset, which is one of the largest phylogenomic datasets to date. We compared wQFM with wQMC, which is the best alternate method for weighted quartet amalgamation, and with ASTRAL, which is one of the most accurate and widely used coalescent-based species tree estimation methods. Our results suggest that wQFM matches or improves upon the accuracy of wQMC and ASTRAL.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Datasets studied in this article and wQFM (in open-source form) are available at https:\/\/github.com\/Mahim1997\/wQFM-2020.<\/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\/btab428","type":"journal-article","created":{"date-parts":[[2021,6,3]],"date-time":"2021-06-03T08:49:33Z","timestamp":1622710173000},"page":"3734-3743","source":"Crossref","is-referenced-by-count":33,"title":["wQFM: highly accurate genome-scale species tree estimation from weighted quartets"],"prefix":"10.1093","volume":"37","author":[{"given":"Mahim","family":"Mahbub","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh"}]},{"given":"Zahin","family":"Wahab","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh"}]},{"given":"Rezwana","family":"Reaz","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9887-4456","authenticated-orcid":false,"given":"M Saifur","family":"Rahman","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5640-0615","authenticated-orcid":false,"given":"Md Shamsuzzoha","family":"Bayzid","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh"}]}],"member":"286","published-online":{"date-parts":[[2021,6,4]]},"reference":[{"key":"2023051608164356300_btab428-B1","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1093\/molbev\/msl170","article-title":"Bayesian estimation of concordance among gene trees","volume":"24","author":"An\u00e9","year":"2007","journal-title":"Mol. 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