A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees

Background 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. Even for binary trees, exact solvers struggle to solve inst...

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Published in:BMC bioinformatics Vol. 15; no. 1; p. 127
Main Authors: Iersel, Leo van, Kelk, Steven, Lekić, Nela, Scornavacca, Celine
Format: Journal Article
Language:English
Published: London BioMed Central 05.05.2014
BioMed Central Ltd
Springer Nature B.V
Subjects:
Algorithms
Analysis
Bioinformatics
Biologists
Biology
Biomedical and Life Sciences
Comparative genomics
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Computer Science
Evolution
Genetic aspects
Hybridization
Hybridization, Genetic
Life Sciences
Methods
Microarrays
Phylogenetics
Phylogeny
Research Article
Software
Phylogenetic networks
Hybridization number
Approximation algorithms
Directed feedback vertex set
ISSN:1471-2105, 1471-2105
Online Access:Get full text
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Summary:Background 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. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 40-50. Results Here we present CycleKiller and NonbinaryCycleKiller , the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations. Conclusions Using simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spin-off from our simulations we also present TerminusEst , which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the NonbinaryCycleKiller algorithm. All three methods are based on extensions of previous theoretical work (SIDMA 26(4):1635-1656, TCBB 10(1):18-25, SIDMA 28(1):49-66) and are publicly available. We also apply our methods to real data.
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ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-15-127