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SMS: Smart Model Selection in PhyML.

Vincent Lefort1, Jean-Emmanuel Longueville1, Olivier Gascuel1,2

  • 1Institut de Biologie Computationnelle, LIRMM, UMR 5506 - CNRS et Université de Montpellier, Montpellier, France.

Molecular Biology and Evolution
|May 5, 2017
PubMed
Summary
This summary is machine-generated.

Selecting the best phylogenetic model is crucial. Our heuristic method speeds up model selection, providing accurate results comparable to existing tools and available via user-friendly interfaces.

Keywords:
AIC and BIC criteriaPhyMLheuristic proceduremodel selectionweb server

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Phylogenetics

Background:

  • Model selection is a critical initial step in phylogenetic analysis.
  • Choosing appropriate substitution matrices and rate models across sites is essential for accurate evolutionary inference.
  • Exhaustive testing of all model combinations can be computationally intensive.

Purpose of the Study:

  • To develop and present a heuristic approach for efficient phylogenetic model selection.
  • To reduce the computational burden associated with identifying optimal evolutionary models.
  • To provide a practical software tool for phylogenetic model selection.

Main Methods:

  • Implementation of heuristic algorithms to approximate optimal model selection.
  • Integration of the heuristic method within the PhyML phylogenetic analysis environment.
  • Development of both command-line and web server interfaces for the "Smart Model Selection" (SMS) software.

Main Results:

  • The heuristic method significantly reduces computation time (approximately by half) compared to exhaustive testing.
  • The results obtained using the heuristic approach are nearly equivalent to those from exhaustive testing.
  • The SMS software demonstrates comparable performance to established model selection tools like ProtTest and jModelTest2.

Conclusions:

  • The developed heuristic method offers an efficient and accurate solution for phylogenetic model selection.
  • The "Smart Model Selection" (SMS) software provides a valuable and accessible tool for researchers in phylogenetics.
  • SMS facilitates streamlined phylogenetic analyses through its integration into existing workflows and user-friendly interfaces.