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.
Computational and Applied Mathematics – Springer Journals
Published: Jun 4, 2018
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