NDLI: Couplet supertree by equivalence partitioning of taxa set and DAG formation

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Couplet supertree by equivalence partitioning of taxa set and DAG formation

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Couplet supertree by equivalence partitioning of taxa set and DAG formation

Content Provider	ACM Digital Library
Author	Bhattacharyya, Sourya Mukhopadhyay, Jayanta
Abstract	From a given set of phylogenetic trees with overlapping taxa sets, a supertree describes evolutionary relationships among the union of their constituent taxa sets. Individual taxa subsets, however, can exhibit conflicting evolutionary relationships for different input trees. Strict consensus supertrees do not include any taxa subset exhibiting conflicts, thus can be $non-plenary^{1}.$ Plenary supertrees, on the other hand, aims to satisfy maximum agreement property, by resolving conflicts with the consensus (most frequent) relation (with respect to the input trees) between corresponding taxa subset. However, satisfying such property is NP hard. Existing studies propose various approximations based on matrix or graph representation, or using subtree level decomposition, for supertree construction. Most of these approaches involve high computational complexity. Further, accuracy of most of these methods need to be improved for application in large biological datasets. Current study presents a supertree construction method, named COSPEDTree, by analyzing couplet (taxa pair) relationships and their conflicts (contradictions) with respect to the source trees. To the best of our knowledge, such couplet based supertree construction is not proposed before. To prioritize the consensus relations for resolving individual taxa pairs, a greedy scoring method is suggested. Selected relations between individual taxa pairs are used to model a Directed Acyclic Graph (DAG), which subsequently generates the final supertree. Performance of COSPEDTree, in terms of lower values of branch dissimilarities between the derived supertree and the candidate source trees, are mostly better or comparable with existing methods. COSPEDTree involves worst case time and space complexities of cubic and quadratic orders, respectively, both of which are best among reference approaches. So, it can be used for large biological datasets. It is hosted in http://telemedik.iitkgp.ernet.in/COSPEDTree_BCB.zip.
Starting Page	259
Ending Page	268
Page Count	10
File Format	PDF
ISBN	9781450328944
DOI	10.1145/2649387.2649388
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2014-09-20
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Supertree Directed acyclic graph (dag) Phylogenetics
Content Type	Text
Resource Type	Article

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