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Building a small and informative phylogenetic supertree
Stockholms universitet, Naturvetenskapliga fakulteten, Matematiska institutionen. The Hong Kong Polytechnic University, Hong Kong.
Antal upphovsmän: 32023 (Engelska)Ingår i: Information and Computation, ISSN 0890-5401, E-ISSN 1090-2651, Vol. 294, artikel-id 105082Artikel i tidskrift (Refereegranskat) 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.

Ort, förlag, år, upplaga, sidor
2023. Vol. 294, artikel-id 105082
Nyckelord [en]
Phylogenetic tree, Supertree, Rooted triplet, Consistency, Approximation algorithm
Nationell ämneskategori
Bioinformatik (beräkningsbiologi)
Identifikatorer
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
Tillgänglig från: 2023-11-01 Skapad: 2023-11-01 Senast uppdaterad: 2023-11-01Bibliografiskt granskad

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Thekkumpadan Puthiyaveedu, Sandhya

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