Building a Small and Informative Phylogenetic Supertree

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  • Jesper Jansson, Department of Computing, The Hong Kong Polytechnic University, Hong Kong
  • Konstantinos Mampentzidis
  • Sandhya Thekkumpadan Puthiyaveedu, Department of Computing, The Hong Kong Polytechnic University, Hong Kong
We combine two fundamental, previously studied optimization problems related to the construction of phylogenetic trees called maximum rooted triplets consistency (MAXRTC) and minimally resolved supertree (MINRS) into a new problem, which we call q-maximum rooted triplets consistency (q-MAXRTC). The input to our new problem is a set R of resolved triplets (rooted, binary phylogenetic trees with three leaves each) and the objective is find a phylogenetic tree with exactly q internal nodes that contains the largest possible number of triplets from R. We first prove that q-MAXRTC is NP-hard even to approximate within a constant ratio for every fixed q>=2, and then develop various polynomial-time approximation algorithms for different values of q. Next, we show experimentally that representing a phylogenetic tree by one having much fewer nodes typically does not destroy too much branching information. As an extreme example, we show that allowing only nine internal nodes is still sufficient to capture on average 80% of the rooted triplets from some recently published trees, each having between 760 and 3081 internal nodes. Finally, to demonstrate the algorithmic advantage of using trees with few internal nodes, we propose a new algorithm for computing the rooted triplet distance between two phylogenetic trees over a leaf label set of size n that runs in O(qn) time, where q is the number of internal nodes in the smaller tree, and is therefore faster than the currently best algorithms for the problem (with O(nlogn) time complexity [SODA 2013, ESA 2017]) whenever q=o(logn).
OriginalsprogEngelsk
Udgivelsesår2019
StatusUdgivet - 2019
BegivenhedWorkshop on Algorithms in Bioinformatics (WABI) 2019 - Conference and Event Center Niagara Falls, Niagara Falls, NY, Buffalo, New York, USA
Varighed: 8 sep. 201910 sep. 2019
https://acm-bcb.org/WABI/2019/

Konference

KonferenceWorkshop on Algorithms in Bioinformatics (WABI) 2019
LokationConference and Event Center Niagara Falls, Niagara Falls, NY
LandUSA
ByBuffalo, New York
Periode08/09/201910/09/2019
Internetadresse

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