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Building a small and informative phylogenetic supertree
Stockholm University, Faculty of Science, Department of Mathematics. The Hong Kong Polytechnic University, Hong Kong.
Number of Authors: 32023 (English)In: Information and Computation, ISSN 0890-5401, E-ISSN 1090-2651, Vol. 294, article id 105082Article in journal (Refereed) Published
Abstract [en]

We combine two fundamental optimization problems related to the construction of phylogenetic trees called maximum rooted triplets consistency and minimally resolved supertree into a new problem, which we call q-maximum rooted triplets consistency (q-MAXRTC). It takes as input a set R of rooted, binary phylogenetic trees with three leaves each and asks for a phylogenetic tree with exactly q internal nodes that contains the largest possible number of trees from R. We prove that q-MAXRTC is NP-hard to approximate within a constant, develop polynomial-time approximation algorithms for different values of q, and show experimentally that representing a phylogenetic tree by one having much fewer nodes typically does not destroy too much branching information. To demonstrate the algorithmic advantage of using trees with few internal nodes, we also propose a new algorithm for computing the rooted triplet distance that is faster than the existing algorithms when restricted to such trees.

Place, publisher, year, edition, pages
2023. Vol. 294, article id 105082
Keywords [en]
Phylogenetic tree, Supertree, Rooted triplet, Consistency, Approximation algorithm
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:su:diva-223434DOI: 10.1016/j.ic.2023.105082ISI: 001082950600001Scopus ID: 2-s2.0-85169921405OAI: oai:DiVA.org:su-223434DiVA, id: diva2:1808755
Available from: 2023-11-01 Created: 2023-11-01 Last updated: 2023-11-01Bibliographically approved

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Thekkumpadan Puthiyaveedu, Sandhya

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