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Model checking software for phylogenetic trees using distribution and database methods

Requeno, José Ignacio ; Colom, José Manuel

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)

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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.

Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Requeno, José Ignacio ; Colom, José Manuel  (2013)  Model checking software for phylogenetic trees using distribution and database methods. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 10(3): Special Issue: Selected extended papers of the 7th International Conference on Practical Applications of Computational Biology and Bioinformatics, Salamanca, Spain, 2013

Online-Journal: http://journal.imbio.de/article.php?aid=229
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2013/5307

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