{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T10:11:27Z","timestamp":1776075087054,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1009960","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,3,21]],"date-time":"2022-03-21T00:00:00Z","timestamp":1647820800000}}],"reference-count":32,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2022,3,9]],"date-time":"2022-03-09T00:00:00Z","timestamp":1646784000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000987","name":"Melbourne Research, University of Melbourne","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000987","id-type":"DOI","asserted-by":"publisher"}]},{"name":"the Xing Lei Scholarship"},{"name":"Professor Maurice H. Belz Fund"},{"name":"Albert Shimmins Fund"},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/R044732\/1"],"award-info":[{"award-number":["EP\/R044732\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>We present a novel algorithm, implemented in the software<jats:italic>ARGinfer<\/jats:italic>, for probabilistic inference of the Ancestral Recombination Graph under the Coalescent with Recombination. Our Markov Chain Monte Carlo algorithm takes advantage of the Succinct Tree Sequence data structure that has allowed great advances in simulation and point estimation, but not yet probabilistic inference. Unlike previous methods, which employ the Sequentially Markov Coalescent approximation,<jats:italic>ARGinfer<\/jats:italic>uses the Coalescent with Recombination, allowing more accurate inference of key evolutionary parameters. We show using simulations that<jats:italic>ARGinfer<\/jats:italic>can accurately estimate many properties of the evolutionary history of the sample, including the topology and branch lengths of the genealogical tree at each sequence site, and the times and locations of mutation and recombination events.<jats:italic>ARGinfer<\/jats:italic>approximates posterior probability distributions for these and other quantities, providing interpretable assessments of uncertainty that we show to be well calibrated.<jats:italic>ARGinfer<\/jats:italic>is currently limited to tens of DNA sequences of several hundreds of kilobases, but has scope for further computational improvements to increase its applicability.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1009960","type":"journal-article","created":{"date-parts":[[2022,3,9]],"date-time":"2022-03-09T18:41:08Z","timestamp":1646851268000},"page":"e1009960","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":34,"title":["Bayesian inference of ancestral recombination graphs"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3813-3477","authenticated-orcid":true,"given":"Ali","family":"Mahmoudi","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2836-8777","authenticated-orcid":true,"given":"Jere","family":"Koskela","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7894-5253","authenticated-orcid":true,"given":"Jerome","family":"Kelleher","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8425-8775","authenticated-orcid":true,"given":"Yao-ban","family":"Chan","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1480-6115","authenticated-orcid":true,"given":"David","family":"Balding","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,3,9]]},"reference":[{"issue":"2","key":"pcbi.1009960.ref001","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":"RR Hudson","year":"1983","journal-title":"Theoretical Population Biology"},{"key":"pcbi.1009960.ref002","first-page":"257","article-title":"An ancestral recombination graph","volume":"87","author":"RC Griffiths","year":"1997","journal-title":"Institute for Mathematics and its Applications"},{"issue":"9","key":"pcbi.1009960.ref003","doi-asserted-by":"crossref","first-page":"1306","DOI":"10.1038\/s41588-019-0492-x","article-title":"From a database of genomes to a forest of evolutionary trees","volume":"51","author":"K Harris","year":"2019","journal-title":"Nature Genetics"},{"key":"pcbi.1009960.ref004","unstructured":"Hubisz M. 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