{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,18]],"date-time":"2026-10-18T06:58:04Z","timestamp":1792306684781,"version":"4.4.0"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2315,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Phylogenetic trees are widely used to display estimates of how groups of species are evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees are obtained for several datasets (e.g. for different genes), then their clusters are often contradicting. Consequently, the set of all clusters of such a dataset cannot be combined into a single phylogenetic tree. Phylogenetic networks are a generalization of phylogenetic trees that can be used to display more complex evolutionary histories, including reticulate events, such as hybridizations, recombinations and horizontal gene transfers. Here, we present the new Cass algorithm that can combine any set of clusters into a phylogenetic network. We show that the networks constructed by Cass are usually simpler than networks constructed by other available methods. Moreover, we show that Cass is guaranteed to produce a network with at most two reticulations per biconnected component, whenever such a network exists. We have implemented Cass and integrated it into the freely available Dendroscope software.<\/jats:p>\n               <jats:p>Contact: \u00a0l.j.j.v.iersel@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq202","type":"journal-article","created":{"date-parts":[[2010,6,7]],"date-time":"2010-06-07T07:28:13Z","timestamp":1275895693000},"page":"i124-i131","source":"Crossref","is-referenced-by-count":56,"title":["Phylogenetic networks do not need to be complex: using fewer reticulations to represent conflicting clusters"],"prefix":"10.1093","volume":"26","author":[{"given":"Leo","family":"van Iersel","sequence":"first","affiliation":[{"name":"1 Department of Mathematics and Statistics, University of Canterbury, Private Bag 4800, Christchurch, New Zealand, 2 Centrum voor Wiskunde en Informatica (CWI), Life Sciences, P.O. Box 94079, 1090 GB Amsterdam, The Netherlands and 3 Center for Bioinformatics ZBIT, T\u00fcbingen University, Sand 14, 72076 T\u00fcbingen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven","family":"Kelk","sequence":"additional","affiliation":[{"name":"1 Department of Mathematics and Statistics, University of Canterbury, Private Bag 4800, Christchurch, New Zealand, 2 Centrum voor Wiskunde en Informatica (CWI), Life Sciences, P.O. Box 94079, 1090 GB Amsterdam, The Netherlands and 3 Center for Bioinformatics ZBIT, T\u00fcbingen University, Sand 14, 72076 T\u00fcbingen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Regula","family":"Rupp","sequence":"additional","affiliation":[{"name":"1 Department of Mathematics and Statistics, University of Canterbury, Private Bag 4800, Christchurch, New Zealand, 2 Centrum voor Wiskunde en Informatica (CWI), Life Sciences, P.O. Box 94079, 1090 GB Amsterdam, The Netherlands and 3 Center for Bioinformatics ZBIT, T\u00fcbingen University, Sand 14, 72076 T\u00fcbingen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Huson","sequence":"additional","affiliation":[{"name":"1 Department of Mathematics and Statistics, University of Canterbury, Private Bag 4800, Christchurch, New Zealand, 2 Centrum voor Wiskunde en Informatica (CWI), Life Sciences, P.O. Box 94079, 1090 GB Amsterdam, The Netherlands and 3 Center for Bioinformatics ZBIT, T\u00fcbingen University, Sand 14, 72076 T\u00fcbingen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2010,6,1]]},"reference":[{"key":"2023012508060100900_B1","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. Math."},{"key":"2023012508060100900_B2","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1177\/117693430700300017","article-title":"A reduction algorithm for computing the hybridization number of two trees","volume":"3","author":"Bordewich","year":"2007","journal-title":"Evol. Bioinform."},{"key":"2023012508060100900_B3","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.tcs.2004.12.012","article-title":"Computing the maximum agreement of phylogenetic networks","volume":"335","author":"Choy","year":"2005","journal-title":"Theor. Comput. Sci."},{"key":"2023012508060100900_B4","author":"Gambette","year":"2009","journal-title":"Who's who in phylogenetic networks, 2009."},{"key":"2023012508060100900_B5","doi-asserted-by":"crossref","first-page":"373","DOI":"10.2307\/3298585","article-title":"Phylogeny and subfamilial classification of the grasses (Poaceae)","volume":"88","author":"Grass Phylogeny Working Group","year":"2001","journal-title":"Ann. Mo. Bot. Gard."},{"key":"2023012508060100900_B6","doi-asserted-by":"crossref","first-page":"1247","DOI":"10.1089\/cmb.2006.0137","article-title":"A decomposition theory for phylogenetic networks and incompatible characters","volume":"14","author":"Gusfield","year":"2007","journal-title":"J. Comput. Biol."},{"key":"2023012508060100900_B7","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1016\/j.dam.2005.05.044","article-title":"An efficiently computed lower bound on the number of recombinations in phylogenetic networks: theory and empirical study","volume":"155","author":"Gusfield","year":"2007","journal-title":"Discrete Appl. Math."},{"key":"2023012508060100900_B8","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1007\/978-3-540-71681-5_15","article-title":"Beyond galled trees - decomposition and computation of galled networks","volume-title":"Research in Computational Molecular Biology (RECOMB)","author":"Huson","year":"2007"},{"key":"2023012508060100900_B9","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1007\/978-3-540-87361-7_25","article-title":"Summarizing multiple gene trees using cluster networks","volume-title":"Algorithms in Bioinformatics (WABI)","author":"Huson","year":"2008"},{"key":"2023012508060100900_B10","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1186\/1471-2105-8-460","article-title":"Dendroscope: an interactive viewer for large phylogenetic trees","volume":"8","author":"Huson","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023012508060100900_B11","doi-asserted-by":"crossref","first-page":"i85","DOI":"10.1093\/bioinformatics\/btp217","article-title":"Computing galled networks from real data","volume":"25","author":"Huson","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012508060100900_B12","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1007\/11415770_20","article-title":"Constructing a smallest refining galled phylogenetic network","volume-title":"Research in Computational Molecular Biology (RECOMB)","author":"Huynh","year":"2005"},{"key":"2023012508060100900_B13","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.tcs.2006.06.022","article-title":"Inferring a level-1 phylogenetic network from a dense set of rooted triplets","volume":"363","author":"Jansson","year":"2006","journal-title":"Theor. Comp. Sci."},{"key":"2023012508060100900_B14","doi-asserted-by":"crossref","first-page":"1098","DOI":"10.1137\/S0097539704446529","article-title":"Algorithms for combining rooted triplets into a galled phylogenetic network","volume":"35","author":"Jansson","year":"2006","journal-title":"SIAM J. Comput."},{"key":"2023012508060100900_B15","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1109\/TCBB.2008.86","article-title":"Hybridisation in nonbinary trees","volume":"6","author":"Linz","year":"2009","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"key":"2023012508060100900_B16","article-title":"Evolutionary phylogenetic networks: models and issues","volume-title":"The Problem Solving Handbook for Computational Biology and Bionformatics","author":"Nakleh","year":"2009"},{"key":"2023012508060100900_B17","volume-title":"Phylogenetic trees from large datasets.","author":"Schmidt","year":"2003"},{"key":"2023012508060100900_B18","first-page":"277","article-title":"Hybridization networks","volume-title":"Reconstructing Evolution - New Mathematical and Computational Advances","author":"Semple","year":"2007"},{"key":"2023012508060100900_B19","first-page":"275","article-title":"Level-kphylogenetic networks are constructable from a dense triplet set in polynomial time","volume":"5577","author":"To","year":"2009","journal-title":"Combinatorial Pattern Matching (CPM)"},{"key":"2023012508060100900_B20","article-title":"Constructing the simplest possible phylogenetic network from triplets","author":"van Iersel","year":"2009","journal-title":"Algorithmica"},{"key":"2023012508060100900_B21","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1109\/TCBB.2009.22","article-title":"Constructing level-2 phylogenetic networks from triplets","volume":"6","author":"van Iersel","year":"2009","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"key":"2023012508060100900_B22","author":"van Iersel","year":"2009","journal-title":"Cass: Combining phylogenetic trees into a phylogenetic network"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/12\/i124\/48858656\/bioinformatics_26_12_i124.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/12\/i124\/48858656\/bioinformatics_26_12_i124.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:09:38Z","timestamp":1674634178000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/12\/i124\/284444"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,6,1]]},"references-count":22,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2010,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq202","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,6,15]]},"published":{"date-parts":[[2010,6,1]]}}}