Speeding Up Phylogenetic Model Checking

Abstract

Model checking is a generic and formal technique that the authors have proposed for the study of properties that emerge from the biological labeling of the states defined over the phylogenetic tree [3] [10]. 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 related subproblems 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 outperformed the results of monolithic model checking and helped us to execute the verification of properties in a real phylogenetic tree. © Springer International Publishing Switzerland 2013.