{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T15:26:45Z","timestamp":1783092405402,"version":"3.54.6"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1011871","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,2,27]],"date-time":"2024-02-27T00:00:00Z","timestamp":1708992000000}}],"reference-count":44,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2024,2,8]],"date-time":"2024-02-08T00:00:00Z","timestamp":1707350400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Natural Science Foundation of China\u2019s Excellent Young Scientists Fund","award":["31922087"],"award-info":[{"award-number":["31922087"]}]},{"name":"Hong Kong Research Grants Council\u2019s General Research Fund","award":["17150816"],"award-info":[{"award-number":["17150816"]}]},{"DOI":"10.13039\/501100016290","name":"Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences","doi-asserted-by":"publisher","award":["COVID1903011-WP1"],"award-info":[{"award-number":["COVID1903011-WP1"]}],"id":[{"id":"10.13039\/501100016290","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Innovation and Technology Commission\u2019s InnoHK funding","award":["D24H"],"award-info":[{"award-number":["D24H"]}]},{"name":"Guangdong Government for the funding supports","award":["2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727"],"award-info":[{"award-number":["2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Massive sequencing of SARS-CoV-2 genomes has urged novel methods that employ existing phylogenies to add new samples efficiently instead of\n                    <jats:italic>de novo<\/jats:italic>\n                    inference. \u2018TIPars\u2019 was developed for such challenge integrating parsimony analysis with pre-computed ancestral sequences. It took about 21 seconds to insert 100 SARS-CoV-2 genomes into a 100k-taxa reference tree using 1.4 gigabytes. Benchmarking on four datasets, TIPars achieved the highest accuracy for phylogenies of moderately similar sequences. For highly similar and divergent scenarios, fully parsimony-based and likelihood-based phylogenetic placement methods performed the best respectively while TIPars was the second best. TIPars accomplished efficient and accurate expansion of phylogenies of both similar and divergent sequences, which would have broad biological applications beyond SARS-CoV-2. 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