Optimal solutions for the balanced minimum evolution problem

Phylogenies are trees representing the evolutionary relationships of a set of species (called taxa). Phylogenies find application in several scientific areas ranging from medical research to drug discovery, epidemiology, systematics and population dynamics. In these applications the available inform...

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Vydáno v:	Computers & operations research Ročník 38; číslo 12; s. 1845 - 1854
Hlavní autoři:	Aringhieri, Roberto, Catanzaro, Daniele, Di Summa, Marco
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	Kidlington Elsevier Ltd 01.12.2011 Elsevier Pergamon Press Inc
Témata:	Algorithms Applied sciences Assignment problem Balanced minimum evolution Balancing Biological and medical sciences Biological evolution Combinatorial optimization Computational biology Dynamical systems Effectiveness studies Epidemiology Evolution Exact sciences and technology Fundamental and applied biological sciences. Psychology General aspects General pharmacology Genetics of eukaryotes. Biological and molecular evolution Logistics Mathematical models Mathematical problems Medical sciences Operational research and scientific management Operational research. Management science Operations research Optimization Optimization algorithms Pharmacology. Drug treatments Phylogenetics Public health. Hygiene Public health. Hygiene-occupational medicine Quadratic assignment Quadratic programming Trees Balanced minimum evolution Quadratic assignment Combinatorial optimization Computational biology Parallel algorithm Tree(graph) Enumeration Assignment problem Scientific application Phylogeny Quadratic programming Epidemiology Location problem Scientific computation Optimal solution Problem solving Parallelism Population dynamics Pharmaceutical industry Bioinformatics Medical application Mathematical programming
ISSN:	0305-0548, 1873-765X, 0305-0548
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Popis
Shrnutí:	Phylogenies are trees representing the evolutionary relationships of a set of species (called taxa). Phylogenies find application in several scientific areas ranging from medical research to drug discovery, epidemiology, systematics and population dynamics. In these applications the available information is usually restricted to the leaves of a phylogeny and is represented by molecular data extracted from the species analyzed. On the contrary, the information about the phylogeny itself is generally missing and must be determined by solving an optimization problem, called the phylogeny estimation problem (PEP), whose versions depend on the criterion used to select a phylogeny among plausible alternatives. In this paper, we investigate one of the most significant versions of the PEP, called the balanced minimum evolution problem. We propose an exact algorithm based on the enumeration of non-isomorphic trees and the subsequent solution of quadratic assignment problems. Furthermore, by exploiting the underlying parallelism of the algorithm, we present a parallel version of the algorithm which shows a linear speed-up with respect to the sequential version. Extensive computational results prove the effectiveness of the proposed algorithms.
Bibliografie:	SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 14 ObjectType-Article-2 content type line 23
ISSN:	0305-0548 1873-765X 0305-0548
DOI:	10.1016/j.cor.2011.02.020