Model checking software for phylogenetic trees using distribution and database methods

• Published in: Journal of integrative bioinformatics 2013-12, Vol.10 (3), p.16-30
• Main Authors: Requeno, José Ignacio, Colom, José Manuel
• Format: Article
• Language: English
• ISSN: 1613-4516; 1613-4516
• DOI: 10.1515/jib-2013-229

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.