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New Heuristics for Rooted Triplet Consistency†
Amirkabir University of Technology (Tehran Polytechnic), 424 Hafez Ave, Tehran, Iran
Bioinformatics Group, School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Niavaran, Tehran, Iran
Shahid Beheshti University, Evin, Tehran 19839-63113, Iran
† An extended abstract of this article has appeared in the proceedings of the Annual International Conference on Bioinformatics and Computational Biology (BICB 2011) in Singapore.
* Author to whom correspondence should be addressed.
Received: 14 April 2013; in revised form: 26 June 2013 / Accepted: 26 June 2013 / Published: 11 July 2013
Abstract: Rooted triplets are becoming one of the most important types of input for reconstructing rooted phylogenies. A rooted triplet is a phylogenetic tree on three leaves and shows the evolutionary relationship of the corresponding three species. In this paper, we investigate the problem of inferring the maximum consensus evolutionary tree from a set of rooted triplets. This problem is known to be APX-hard. We present two new heuristic algorithms. For a given set of m triplets on n species, the FastTree algorithm runs in O(m + α(n)n2) time, where α(n) is the functional inverse of Ackermann’s function. This is faster than any other previously known algorithms, although the outcome is less satisfactory. The Best Pair Merge with Total Reconstruction (BPMTR) algorithm runs in O(mn3) time and, on average, performs better than any other previously known algorithms for this problem.
Keywords: phylogenetic tree; rooted triplet; consensus tree; approximation algorithm
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MDPI and ACS Style
Jahangiri, S., Tazehkand; Hashemi, S.N.; Poormohammadi, H. New Heuristics for Rooted Triplet Consistency. Algorithms 2013, 6, 396-406.
Jahangiri S, Tazehkand, Hashemi SN, Poormohammadi H. New Heuristics for Rooted Triplet Consistency. Algorithms. 2013; 6(3):396-406.
Jahangiri, Soheil, Tazehkand; Hashemi, Seyed N.; Poormohammadi, Hadi. 2013. "New Heuristics for Rooted Triplet Consistency." Algorithms 6, no. 3: 396-406.