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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan

4 Issues per year


CiteScore 2016: 0.93

SCImago Journal Rank (SJR) 2016: 0.416

Open Access
Online
ISSN
1613-4516
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Volume 10, Issue 3

Issues

Model checking software for phylogenetic trees using distribution and database methods

José Ignacio Requeno
  • Corresponding author
  • Department of Computer Science and Systems Engineering (DIIS), Universidad de Zaragoza, C/ María de Luna 1, 50018 Zaragoza, Spain
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  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ José Manuel Colom
  • Department of Computer Science and Systems Engineering (DIIS), Universidad de Zaragoza, C/ María de Luna 1, 50018 Zaragoza, Spain
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2013-229

Summary

Model checking, a generic and formal paradigm stemming from computer science based on temporal logics, has been proposed for the study of biological properties that emerge from the labeling of the states defined over the phylogenetic tree. This strategy allows us to use generic software tools already present in the industry. However, the performance of traditional model checking is penalized when scaling the system for large phylogenies. To this end, two strategies are presented here. The first one consists of partitioning the phylogenetic tree into a set of subgraphs each one representing a subproblem to be verified so as to speed up the computation time and distribute the memory consumption. The second strategy is based on uncoupling the information associated to each state of the phylogenetic tree (mainly, the DNA sequence) and exporting it to an external tool for the management of large information systems. The integration of all these approaches outperforms the results of monolithic model checking and helps us to execute the verification of properties in a real phylogenetic tree.

About the article

Published Online: 2016-10-18

Published in Print: 2013-12-01


Citation Information: Journal of Integrative Bioinformatics, Volume 10, Issue 3, Pages 16–30, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2013-229.

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© 2013 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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