{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T21:51:41Z","timestamp":1775857901571,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2022,9,12]],"date-time":"2022-09-12T00:00:00Z","timestamp":1662940800000},"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\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IIS-1845967"],"award-info":[{"award-number":["IIS-1845967"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Species tree inference from multi-copy gene trees has long been a challenge in phylogenomics. The recent method ASTRAL-Pro has made strides by enabling multi-copy gene family trees as input and has been quickly adopted. Yet, its scalability, especially memory usage, needs to improve to accommodate the ever-growing dataset size.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present ASTRAL-Pro 2, an ultrafast and memory efficient version of ASTRAL-Pro that adopts a placement-based optimization algorithm for significantly better scalability without sacrificing accuracy.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code and binary files are publicly available at https:\/\/github.com\/chaoszhang\/ASTER; data are available at https:\/\/github.com\/chaoszhang\/A-Pro2_data.<\/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\/btac620","type":"journal-article","created":{"date-parts":[[2022,9,10]],"date-time":"2022-09-10T00:38:14Z","timestamp":1662770294000},"page":"4949-4950","source":"Crossref","is-referenced-by-count":100,"title":["ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4222-9968","authenticated-orcid":false,"given":"Chao","family":"Zhang","sequence":"first","affiliation":[{"name":"Bioinformatics and Systems Biology, UC San Diego , La Jolla, CA 92093, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5410-1518","authenticated-orcid":false,"given":"Siavash","family":"Mirarab","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, UC San Diego , La Jolla, CA 92093, USA"}]}],"member":"286","published-online":{"date-parts":[[2022,9,12]]},"reference":[{"key":"2023091205384397500_btac620-B1","author":"Hill","year":"2020"},{"key":"2023091205384397500_btac620-B2","doi-asserted-by":"crossref","first-page":"1532","DOI":"10.1093\/bioinformatics\/btab875","article-title":"Completing gene trees without species trees in sub-quadratic time","volume":"38","author":"Mai","year":"2022","journal-title":"Bioinformatics"},{"key":"2023091205384397500_btac620-B3","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1146\/annurev-ecolsys-012121-095340","article-title":"Multispecies coalescent: theory and applications in phylogenetics","volume":"52","author":"Mirarab","year":"2021","journal-title":"Annu. 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