A Practical Approximation Algorithm for Solving Massive Instances of Hybridization Number

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• 作者：Leo van Iersel (1) l.j.j.v.iersel@gmail.com
  Steven Kelk (2) steven.kelk@maastrichtuniversity.nl
  Nela Leki? (2) nela.lekic@maastrichtuniversity.nl
  Celine Scornavacca (3) celine.scornavacca@univ-montp2.fr
• 刊名：Lecture Notes in Computer Science
• 出版年：2012
• 出版时间：2012
• 年：2012
• 卷：7534
• 期：1
• 页码：430-440
• 全文大小：187.7 KB
• 参考文献：1. Albrecht, B., Scornavacca, C., Cenci, A., Huson, D.H.: Fast computation of minimum hybridization networks. Bioinformatics 28(2), 191–197 (2012)
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• 作者单位：1. Centrum Wiskunde & Informatica (CWI), P.O. Box 94079, 1090 GB Amsterdam, The Netherlands2. Department of Knowledge Engineering (DKE), Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands3. Institut des Sciences de l’Evolution (ISEM, UMR 5554 CNRS), Université Montpellier?II, Place E. Bataillon - CC 064, 34095 Montpellier Cedex 5, France
• ISSN：1611-3349

文摘

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.