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Conference Paper: Reconstructing k-Reticulated Phylogenetic Network from a Set of Gene Trees

TitleReconstructing k-Reticulated Phylogenetic Network from a Set of Gene Trees
Authors
Issue Date2013
PublisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/
Citation
The 9th International Symposium on Bioinformatics Research and Applications (ISBRA 2013), Charlotte, NC., 20-22 May 2013. In Lecture Notes in Computer Science, 2013, v. 7875, p. 112-124 How to Cite?
AbstractThe time complexity of existing algorithms for reconstructing a level-x phylogenetic network increases exponentially in x. In this paper, we propose a new classification of phylogenetic networks called k-reticulated network. A k-reticulated network can model all level-k networks and some level-x networks with x > k. We design algorithms for reconstructing k-reticulated network (k = 1 or 2) with minimum number of hybrid nodes from a set of m binary trees, each with n leaves in O(mn 2) time. The implication is that some level-x networks with x > k can now be reconstructed in a faster way. We implemented our algorithm (ARTNET) and compared it with CMPT. We show that ARTNET outperforms CMPT in terms of running time and accuracy. We also consider the case when there does not exist a 2-reticulated network for the input trees. We present an algorithm computing a maximum subset of the species set so that a new set of subtrees can be combined into a 2-reticulated network.
DescriptionLecture Notes in Computer Science v. 7875 entitled: Bioinformatics research and applications : 9th international symposium, ISBRA 2013 ... proceedings
Persistent Identifierhttp://hdl.handle.net/10722/191051
ISBN
ISSN
2005 Impact Factor: 0.402
2015 SCImago Journal Rankings: 0.252

 

DC FieldValueLanguage
dc.contributor.authorVu, Hen_US
dc.contributor.authorChin, FYLen_US
dc.contributor.authorHon, WKen_US
dc.contributor.authorLeung, HCMen_US
dc.contributor.authorSadakane, Ken_US
dc.contributor.authorSung, WKen_US
dc.contributor.authorYiu, SMen_US
dc.date.accessioned2013-09-17T16:13:34Z-
dc.date.available2013-09-17T16:13:34Z-
dc.date.issued2013en_US
dc.identifier.citationThe 9th International Symposium on Bioinformatics Research and Applications (ISBRA 2013), Charlotte, NC., 20-22 May 2013. In Lecture Notes in Computer Science, 2013, v. 7875, p. 112-124en_US
dc.identifier.isbn9783642380358-
dc.identifier.issn0302-9743-
dc.identifier.urihttp://hdl.handle.net/10722/191051-
dc.descriptionLecture Notes in Computer Science v. 7875 entitled: Bioinformatics research and applications : 9th international symposium, ISBRA 2013 ... proceedings-
dc.description.abstractThe time complexity of existing algorithms for reconstructing a level-x phylogenetic network increases exponentially in x. In this paper, we propose a new classification of phylogenetic networks called k-reticulated network. A k-reticulated network can model all level-k networks and some level-x networks with x > k. We design algorithms for reconstructing k-reticulated network (k = 1 or 2) with minimum number of hybrid nodes from a set of m binary trees, each with n leaves in O(mn 2) time. The implication is that some level-x networks with x > k can now be reconstructed in a faster way. We implemented our algorithm (ARTNET) and compared it with CMPT. We show that ARTNET outperforms CMPT in terms of running time and accuracy. We also consider the case when there does not exist a 2-reticulated network for the input trees. We present an algorithm computing a maximum subset of the species set so that a new set of subtrees can be combined into a 2-reticulated network.-
dc.languageengen_US
dc.publisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/-
dc.relation.ispartofLecture Notes in Computer Scienceen_US
dc.rightsThe original publication is available at www.springerlink.com-
dc.titleReconstructing k-Reticulated Phylogenetic Network from a Set of Gene Treesen_US
dc.typeConference_Paperen_US
dc.identifier.emailChin, FYL: chin@cs.hku.hken_US
dc.identifier.emailLeung, HCM: cmleung2@cs.hku.hken_US
dc.identifier.emailYiu, SM: smyiu@cs.hku.hken_US
dc.identifier.authorityChin, FYL=rp00105en_US
dc.identifier.authorityLeung, HCM=rp00144en_US
dc.identifier.authorityYiu, SM=rp00207en_US
dc.identifier.doi10.1007/978-3-642-38036-5_14-
dc.identifier.scopuseid_2-s2.0-84883319157-
dc.identifier.hkuros223605en_US
dc.identifier.hkuros238679-
dc.identifier.volume7875-
dc.identifier.spage112en_US
dc.identifier.epage124en_US
dc.publisher.placeGermany-
dc.customcontrol.immutablesml 151014-

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