A Faster FPT Algorithm for the Maximum Agreement Forest Problem

Authors:
Michael Hallett;Catherine Mccartin
Affiliations:
McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada H3A 2A7;Institute of Information Sciences and Technology, Massey University, Palmerston North, New Zealand
Venue:
Theory of Computing Systems
Year:
2007

Citing 0
Cited 6

A 3-approximation algorithm for the subtree distance between phylogenies

Journal of Discrete Algorithms
A unifying view on approximation and FPT of agreement forests

WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
On the Complexity of uSPR Distance

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Parameterized algorithms

Algorithms and theory of computation handbook
A parameterized complexity tutorial

LATA'12 Proceedings of the 6th international conference on Language and Automata Theory and Applications
A basic parameterized complexity primer

The Multivariate Algorithmic Revolution and Beyond

Quantified Score

Hi-index	0.00

Visualization

Abstract

Given two unrooted, binary trees, T1 and T2, leaf labelled bijectively by a set of species L, the Maximum Agreement Forest (MAF) problem asks to find a minimum cardinality collection F = {t1, ..., tk} of phylogenetic trees where each element of F is a subtree of both T1 and T2, the elements of F are pairwise disjoint, and the leaf labels for the elements of F partition the leaf label set L. We give an efficient fixed-parameter tractable (FPT) algorithm for the MAF problem, significantly improving on an FPT algorithm given in [2]. Whereas the algorithm from [2] has a running time of O(k3k) + p(|L|), our algorithm runs in time O(4k · k5) + p(|L|), where k bounds the size of the agreement forest and p(·) is a low order polynomial.