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Evaluation of properties over phylogenetic trees using stochastic logics.

José Ignacio Requeno1, José Manuel Colom2

  • 1Department of Computer Science and Systems Engineering (DIIS), Universidad de Zaragoza, C/ María de Luna 1, Zaragoza, 50018, Spain. nrequeno@unizar.es.

BMC Bioinformatics
|June 16, 2016
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Summary

This study extends phylogenetic tree analysis by incorporating quantitative data using probabilistic model checking. This approach enhances the accuracy and scope of evolutionary insights derived from phylogenetic models.

Keywords:
DNA mutation modelsMaximum likelihoodModel checkingPhylogeneticsStochastic temporal logic

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Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Formal Methods

Background:

  • Model checking, using temporal logics, has been applied to phylogenetic trees for qualitative information extraction.
  • Previous methods were limited to qualitative aspects, lacking the ability to handle quantitative data like time or probability.

Purpose of the Study:

  • To extend phylogenetic model checking to incorporate and analyze quantitative information, such as time and probability.
  • To develop new methods for analyzing properties not previously addressable in phylogenetic analysis.

Main Methods:

  • Applied probabilistic continuous-time extensions of model checking to phylogenetics.
  • Reinterpreted qualitative properties into a numerical framework.
  • Utilized the PRISM model checking tool for analyzing phylogenies and computing maximum likelihoods.
  • Adapted software for optimizing maximum likelihood computations.

Main Results:

  • Successfully incorporated quantitative information (time, probability) into phylogenetic model checking.
  • Enabled the analysis of new, quantitative properties, including the likelihood of tree topologies under mutation models.
  • Achieved optimized computation of maximum likelihoods for phylogenetic trees using the PRISM tool.

Conclusions:

  • Probabilistic model checking offers a robust and readable framework for quantitative analysis of phylogenetic trees.
  • The use of model checking tools simplifies complex computational aspects for biologists.
  • The approach is demonstrated to be feasible and effective through benchmark analyses.