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A Heuristic for the Live Parsimony Problem

  • Rogério Güths
  • Guilherme P. Telles
  • Maria Emilia M. T. Walter
  • Nalvo F. AlmeidaEmail author
Conference paper
Part of the Communications in Computer and Information Science book series (CCIS, volume 881)

Abstract

Live Phylogeny generalizes the phylogeny theory by admitting living ancestors among the taxonomic objects. This theory suits cases of fast-evolving species like virus, and phylogenies of non-biological objects like documents, images and database records. In character-based live phylogeny, the input is a matrix with n objects and m characters, such each position ij keeps the state of character j for the object i. The output is a tree where the input objects are represented as leaves or internal nodes labeled with a string of m symbols, representing the state of the characters. The goal is to obtain a tree with the minimal number of state changes along the edges, considering all characters, called the most parsimonious tree. In this paper we analyze problems related to most parsimonious tree using Live Phylogeny. We propose an improvement to a previously presented branch-and-bound algorithm and also a new heuristic for the problem. We present the results of experiments with a set of 20 Zika virus genome sequences, comparing the performance of our heuristic.

Keywords

Phylogeny Character state phylogeny Live phylogeny Parsimony Algorithms 

Notes

Acknowledgments

RG and NFA thank Fundect grants TO141/2016 and TO 007/2015. NFA also thanks CNPq grants 305857/2013-4, 473221/2013-6 and CAPES grant 3377/2013. GPT acknowledges CNPq grant 310685/2015-0. MEMT thanks CNPq grant 308524/2015-2.

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Rogério Güths
    • 1
  • Guilherme P. Telles
    • 2
  • Maria Emilia M. T. Walter
    • 3
  • Nalvo F. Almeida
    • 1
    Email author
  1. 1.School of ComputingFederal University of Mato Grosso do SulCampo GrandeBrazil
  2. 2.Institute of ComputingUniversity of CampinasCampinasBrazil
  3. 3.Department of Computer ScienceUniversity of BrasiliaBrasiliaBrazil

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