Parameterized Complexity Theory (Texts in Theoretical Computer Science. An EATCS Series)
Parameterized Complexity Theory (Texts in Theoretical Computer Science. An EATCS Series)
Computing the minimum number of hybridization events for a consistent evolutionary history
Discrete Applied Mathematics
The maximum agreement forest problem: Approximation algorithms and computational experiments
Theoretical Computer Science
Mathematics of Evolution and Phylogeny
Mathematics of Evolution and Phylogeny
Bioinformatics
Phylogenetic Networks: Concepts, Algorithms and Applications
Phylogenetic Networks: Concepts, Algorithms and Applications
Algorithms for Reticulate Networks of Multiple Phylogenetic Trees
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fast FPT algorithms for computing rooted agreement forests: theory and experiments
SEA'10 Proceedings of the 9th international conference on Experimental Algorithms
Fast computation of minimum hybridization networks
Bioinformatics
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Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. In practice, exact solvers struggle to solve instances with reticulation number larger than 40. For such instances, one has to resort to heuristics and approximation algorithms. Here we present the algorithm CycleKiller which is the first approximation algorithm that can produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations. Theoretically, the algorithm is an exponential-time 2-approximation (or 4-approximation in its fastest mode). However, using simulations we demonstrate that in practice the algorithm runs quickly for large and difficult instances, producing solutions within one percent of optimality. An implementation of this algorithm, which extends the theoretical work of [14], has been made publicly available.