PULLPRU: a practical approach to estimate phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion

PULLPRU: a practical approach to estimate phylogenies from single nucleotide polymorphism... Comp. Appl. Math. https://doi.org/10.1007/s40314-018-0638-y PULLPRU: a practical approach to estimate phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion 1 1 2 R. Feizabadi · M. Bagherian · H. R. Vaziri · M. Salahi Received: 5 April 2017 / Revised: 29 April 2018 / Accepted: 2 May 2018 © SBMAC - Sociedade Brasileira de Matemática Aplicada e Computacional 2018 Abstract Phylogeny estimation has been the subject of several researches due to its sig- nificant importance and numerous applications. The aim of this research is to study the phylogeny estimation from Single Nucleotide Polymorphism (SNP) haplotypes under the maximum parsimony criterion (MPPEP-SNP). Previous exact methods have modeled the mentioned problem as a Mixed Integer Programming (MIP) problem. Since the problem, in general, proved to be NP-hard which causes MIP models to take long runtime for solving large-scale instances, the need for non-exact methods is obvious. In this paper, the authors propose a heuristic algorithm that attempts to find the MPPEP-SNP solution in several stages by solving a specific MIP model in each stage. Created based on network flows formulation, MIP models appearing in each stage are very small; therefore, their exact solutions could be found practically very fast. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Computational and Applied Mathematics Springer Journals

PULLPRU: a practical approach to estimate phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion

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Publisher
Springer International Publishing
Copyright
Copyright © 2018 by SBMAC - Sociedade Brasileira de Matemática Aplicada e Computacional
Subject
Mathematics; Applications of Mathematics; Computational Mathematics and Numerical Analysis; Mathematical Applications in the Physical Sciences; Mathematical Applications in Computer Science
ISSN
0101-8205
eISSN
1807-0302
D.O.I.
10.1007/s40314-018-0638-y
Publisher site
See Article on Publisher Site

Abstract

Comp. Appl. Math. https://doi.org/10.1007/s40314-018-0638-y PULLPRU: a practical approach to estimate phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion 1 1 2 R. Feizabadi · M. Bagherian · H. R. Vaziri · M. Salahi Received: 5 April 2017 / Revised: 29 April 2018 / Accepted: 2 May 2018 © SBMAC - Sociedade Brasileira de Matemática Aplicada e Computacional 2018 Abstract Phylogeny estimation has been the subject of several researches due to its sig- nificant importance and numerous applications. The aim of this research is to study the phylogeny estimation from Single Nucleotide Polymorphism (SNP) haplotypes under the maximum parsimony criterion (MPPEP-SNP). Previous exact methods have modeled the mentioned problem as a Mixed Integer Programming (MIP) problem. Since the problem, in general, proved to be NP-hard which causes MIP models to take long runtime for solving large-scale instances, the need for non-exact methods is obvious. In this paper, the authors propose a heuristic algorithm that attempts to find the MPPEP-SNP solution in several stages by solving a specific MIP model in each stage. Created based on network flows formulation, MIP models appearing in each stage are very small; therefore, their exact solutions could be found practically very fast.

Journal

Computational and Applied MathematicsSpringer Journals

Published: Jun 4, 2018

References

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