Graph-Based Algorithms for Boolean Function Manipulation
IEEE Transactions on Computers
IEEE Transactions on Software Engineering - Special issue on formal methods in software practice
Probabilistic Simulations for Probabilistic Processes
CONCUR '94 Proceedings of the Concurrency Theory
CAV '00 Proceedings of the 12th International Conference on Computer Aided Verification
NuSMV 2: An OpenSource Tool for Symbolic Model Checking
CAV '02 Proceedings of the 14th International Conference on Computer Aided Verification
Design and Synthesis of Synchronization Skeletons Using Branching-Time Temporal Logic
Logic of Programs, Workshop
Proceedings of the Conference on Logic of Programs
Logics and Models of Real Time: A Survey
Proceedings of the Real-Time: Theory in Practice, REX Workshop
Efficient On-the-Fly Model Checking for CTL
LICS '95 Proceedings of the 10th Annual IEEE Symposium on Logic in Computer Science
Parametric Quantitative Temporal Reasoning
LICS '99 Proceedings of the 14th Annual IEEE Symposium on Logic in Computer Science
The AxML program family for maximum likelihood-based phylogenetic tree inference: Research Articles
Concurrency and Computation: Practice & Experience - High Performance Computational Biology
Principles of Model Checking (Representation and Mind Series)
Principles of Model Checking (Representation and Mind Series)
25 Years of Model Checking: History, Achievements, Perspectives
25 Years of Model Checking: History, Achievements, Perspectives
Temporal Logic Query Checking: A Tool for Model Exploration
IEEE Transactions on Software Engineering
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Parallel and distributed model checking in Eddy
International Journal on Software Tools for Technology Transfer (STTT)
Model Checking Timed and Stochastic Properties with CSL^{TA}
IEEE Transactions on Software Engineering
A Bayesian Approach to Model Checking Biological Systems
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
DiVinE: Parallel Distributed Model Checker
PDMC-HIBI '10 Proceedings of the 2010 Ninth International Workshop on Parallel and Distributed Methods in Verification, and Second International Workshop on High Performance Computational Systems Biology
Phylogenetic Networks: Concepts, Algorithms and Applications
Phylogenetic Networks: Concepts, Algorithms and Applications
PRISM 4.0: verification of probabilistic real-time systems
CAV'11 Proceedings of the 23rd international conference on Computer aided verification
PVESTA: a parallel statistical model checking and quantitative analysis tool
CALCO'11 Proceedings of the 4th international conference on Algebra and coalgebra in computer science
On Parameter Synthesis by Parallel Model Checking
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Predicting protein folding kinetics via temporal logic model checking
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
| Hi-index | 0.00 |
The need for general-purpose algorithms for studying biological properties in phylogenetics motivates research into formal verification frameworks. Researchers can focus their efforts exclusively on evolution trees and property specifications. To this end, model checking, a mature automated verification technique originating in computer science, is applied to phylogenetic analysis. Our approach is based on three cornerstones: a logical modeling of the evolution with transition systems; the specification of both phylogenetic properties and trees using flexible temporal logic formulas; and the verification of the latter by means of automated computer tools. The most conspicuous result is the inception of a formal framework which allows for a symbolic manipulation of biological data (based on the codification of the taxa). Additionally, different logical models of evolution can be considered, complex properties can be specified in terms of the logical composition of others, and the refinement of unfulfilled properties as well as the discovery of new properties can be undertaken by exploiting the verification results. Some experimental results using a symbolic model verifier support the feasibility of the approach.