{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,13]],"date-time":"2025-12-13T07:01:07Z","timestamp":1765609267530},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2004,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Comparing gene content between species can be a useful approach for reconstructing phylogenetic trees. In this paper, we derive a maximum-likelihood estimation of evolutionary distance between species under a simple model of gene genesis and gene loss. Using simulated data on a biological tree with 107 taxa (and on a number of randomly generated trees), we compare the accuracy of tree reconstruction using this ML distance measure to an earlier ad hoc distance. We then compare these distance-based approaches to a character-based tree reconstruction method (Dollo parsimony) which seems well suited to the analysis of gene content data. To simplify simulations, we give a formal proof of the well-known \u2018fact\u2019 that the Dollo parsimony score is independent of the choice of root. Our results show a consistent trend, with the character-based method and ML distance measure outperforming the earlier ad hoc distance method.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.ab.informatik.uni-tuebingen.de\/software\/genecontent\/welcome_en.html<\/jats:p>","DOI":"10.1093\/bioinformatics\/bth198","type":"journal-article","created":{"date-parts":[[2004,3,30]],"date-time":"2004-03-30T01:34:06Z","timestamp":1080610446000},"page":"2044-2049","source":"Crossref","is-referenced-by-count":95,"title":["Phylogenetic trees based on gene content"],"prefix":"10.1093","volume":"20","author":[{"given":"Daniel H.","family":"Huson","sequence":"first","affiliation":[]},{"given":"Mike","family":"Steel","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2004,3,25]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/13\/2044\/48905794\/bioinformatics_20_13_2044.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/13\/2044\/48905794\/bioinformatics_20_13_2044.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T16:31:25Z","timestamp":1674664285000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/20\/13\/2044\/241946"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,3,25]]},"references-count":0,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2004,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bth198","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2004,9,1]]},"published":{"date-parts":[[2004,3,25]]}}}