{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:08:11Z","timestamp":1773274091233,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivations: When reticulation events occur, the evolutionary history of a set of existing species can be represented by a hybridization network instead of an evolutionary tree. When studying the evolutionary history of a set of existing species, one can obtain a phylogenetic tree of the set of species with high confidence by looking at a segment of sequences or a set of genes. When looking at another segment of sequences, a different phylogenetic tree can be obtained with high confidence too. This indicates that reticulation events may occur. Thus, we have the following problem: given two rooted phylogenetic trees on a set of species that correctly represent the tree-like evolution of different parts of their genomes, what is the hybridization network with the smallest number of reticulation events to explain the evolution of the set of species under consideration?<\/jats:p>\n               <jats:p>Results: We develop a program, named HybridNet, for constructing a hybridization network with the minimum number of reticulate vertices from two input trees. We first implement the O(3dn)-time algorithm by Whidden et al. for computing a maximum (acyclic) agreement forest. Our program can output all the maximum (acyclic) agreement forests. We then augment the program so that it can construct an optimal hybridization network for each given maximum acyclic agreement forest. To our knowledge, this is the first time that optimal hybridization networks can be rapidly constructed.<\/jats:p>\n               <jats:p>Availability: The program is available for non-commercial use, at http:\/\/www.cs.cityu.edu.hk\/\u223clwang\/software\/Hn\/treeComp.html<\/jats:p>\n               <jats:p>Contact: \u00a0zzchen@mail.dendai.ac.jp; lwang@cs.cityu.edu.hk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq548","type":"journal-article","created":{"date-parts":[[2010,9,26]],"date-time":"2010-09-26T00:14:03Z","timestamp":1285460043000},"page":"2912-2913","source":"Crossref","is-referenced-by-count":23,"title":["HybridNET: a tool for constructing hybridization networks"],"prefix":"10.1093","volume":"26","author":[{"given":"Zhi-Zhong","family":"Chen","sequence":"first","affiliation":[{"name":"1 Department of Mathematical Sciences, Tokyo Denki University, Ishizaka, Hatoyama, Hiki, Saitama 359-0394, Japan and 2Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong"}]},{"given":"Lusheng","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Mathematical Sciences, Tokyo Denki University, Ishizaka, Hatoyama, Hiki, Saitama 359-0394, Japan and 2Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong"}]}],"member":"286","published-online":{"date-parts":[[2010,9,24]]},"reference":[{"key":"2023012507554959100_B1","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1007\/s00285-005-0315-9","article-title":"Bounding the number of hybridisation events for a consistent evolutionary history","volume":"51","author":"Baroni","year":"2005","journal-title":"J. Math. Biol."},{"key":"2023012507554959100_B2","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1186\/1471-2148-6-15","article-title":"Phylogenetic identification of lateral genetic transfer events","volume":"6","author":"Beiko","year":"2006","journal-title":"BMC Evol. Biol."},{"key":"2023012507554959100_B3","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1007\/s00026-004-0229-z","article-title":"On the computational complexity of the rooted subtree prune and regraft distance","volume":"8","author":"Bordewich","year":"2005","journal-title":"Ann. Combinatorics"},{"key":"2023012507554959100_B4","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1016\/j.dam.2006.08.008","article-title":"Computing the minimum number of hybridization events for a consistent evolutionary history","volume":"155","author":"Bordewich","year":"2007","journal-title":"Discrete Appl. 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