{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T14:52:52Z","timestamp":1775227972703,"version":"3.50.1"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2020,10,8]],"date-time":"2020-10-08T00:00:00Z","timestamp":1602115200000},"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\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 GM117590"],"award-info":[{"award-number":["R01 GM117590"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Biological Mathematical Sciences","award":["2P20GM103395"],"award-info":[{"award-number":["2P20GM103395"]}]},{"name":"NIGMS Institutional Development Award"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>MSCquartets is an R package for species tree hypothesis testing, inference of species trees and inference of species networks under the Multispecies Coalescent model of incomplete lineage sorting and its network analog. Input for these analyses are collections of metric or topological locus trees which are then summarized by the quartets displayed on them. Results of hypothesis tests at user-supplied levels are displayed in a simplex plot by color-coded points. The package implements the QDC and WQDC algorithms for topological and metric species tree inference, and the NANUQ algorithm for level-1 topological species network inference, all of which give statistically consistent estimators under the model.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>MSCquartets is available through the Comprehensive R Archive Network: https:\/\/CRAN.R-project.org\/package=MSCquartets.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa868","type":"journal-article","created":{"date-parts":[[2020,9,23]],"date-time":"2020-09-23T15:14:32Z","timestamp":1600874072000},"page":"1766-1768","source":"Crossref","is-referenced-by-count":67,"title":["MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9921-1091","authenticated-orcid":false,"given":"John A","family":"Rhodes","sequence":"first","affiliation":[{"name":"Department of Mathematics and Statistics, University of Alaska Fairbanks , Fairbanks, AK 99775-6660, USA"}]},{"given":"Hector","family":"Ba\u00f1os","sequence":"additional","affiliation":[{"name":"School of Mathematics, Georgia Institute of Technology , Atlanta, GA 30332-0160, USA"}]},{"given":"Jonathan D","family":"Mitchell","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, University of Alaska Fairbanks , Fairbanks, AK 99775-6660, USA"},{"name":"Unit\u00e9 Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS , Paris, France"}]},{"given":"Elizabeth S","family":"Allman","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, University of Alaska Fairbanks , Fairbanks, AK 99775-6660, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,10,8]]},"reference":[{"key":"2023051709455941600_btaa868-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13015-019-0159-2","article-title":"NANUQ: a method for inferring species networks from gene trees under the coalescent model","volume":"14","author":"Allman","year":"2019","journal-title":"Algorithms Mol. 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