{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,18]],"date-time":"2026-01-18T01:40:43Z","timestamp":1768700443538,"version":"3.49.0"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,28]],"date-time":"2022-12-28T00:00:00Z","timestamp":1672185600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Klaus Tschira Foundation and by DFG","award":["STA 860\/6-2"],"award-info":[{"award-number":["STA 860\/6-2"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Missing data and incomplete lineage sorting (ILS) are two major obstacles to accurate species tree inference. Gene tree summary methods such as ASTRAL and ASTRID have been developed to account for ILS. However, they can be severely affected by high levels of missing data.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present Asteroid, a novel algorithm that infers an unrooted species tree from a set of unrooted gene trees. We show on both empirical and simulated datasets that Asteroid is substantially more accurate than ASTRAL and ASTRID for very high proportions (&amp;gt;80%) of missing data. Asteroid is several orders of magnitude faster than ASTRAL for datasets that contain thousands of genes. It offers advanced features such as parallelization, support value computation and support for multi-copy and multifurcating gene trees.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>Asteroid is freely available at https:\/\/github.com\/BenoitMorel\/Asteroid.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac832","type":"journal-article","created":{"date-parts":[[2022,12,28]],"date-time":"2022-12-28T10:02:59Z","timestamp":1672221779000},"source":"Crossref","is-referenced-by-count":18,"title":["Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6286-4419","authenticated-orcid":false,"given":"Benoit","family":"Morel","sequence":"first","affiliation":[{"name":"Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies , Heidelberg 69118, Germany"},{"name":"Institute for Theoretical Informatics, Karlsruhe Institute of Technology , Karlsruhe 76131, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tom A","family":"Williams","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of Bristol , Bristol BS8, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0353-0691","authenticated-orcid":false,"given":"Alexandros","family":"Stamatakis","sequence":"additional","affiliation":[{"name":"Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies , Heidelberg 69118, Germany"},{"name":"Institute for Theoretical Informatics, Karlsruhe Institute of Technology , Karlsruhe 76131, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,12,28]]},"reference":[{"key":"2023011314464506600_btac832-B1","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1093\/sysbio\/sys078","article-title":"Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice","volume":"62","author":"Aberer","year":"2013","journal-title":"Syst. 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