Abstract
The need for general methods to verify biological properties in phylogenetics motivates research in formal frameworks so that biologists can focus their efforts exclusively in evolution modeling and property specification. Model checking is proposed to this end. Three pillars found this approach: modeling evolution dynamics as transition systems; specifying phylogenetic properties using temporal logic formulae; and verifying the former by means of automated computer tools. As prominent advantages for studying biological properties under our approach, different models of evolution can be considered, complex properties can be specified as the logical composition of others, and the refinement of unfulfilled properties as well as the discovery of new ones can be undertaken by exploiting the results of verification. Preliminary experimental results using the Cadence Symbolic Model Verifier support the feasibility of the methodology.
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Requeno, J.I., Blanco, R., de Miguel Casado, G., Colom, J.M. (2011). Phylogenetic Analysis Using an SMV Tool. In: Rocha, M.P., RodrÃguez, J.M.C., Fdez-Riverola, F., Valencia, A. (eds) 5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011). Advances in Intelligent and Soft Computing, vol 93. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-19914-1_23
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DOI: https://doi.org/10.1007/978-3-642-19914-1_23
Publisher Name: Springer, Berlin, Heidelberg
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