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Related Experiment Videos

Automated phylogenetic detection of recombination using a genetic algorithm.

Sergei L Kosakovsky Pond1, David Posada, Michael B Gravenor

  • 1Department of Pathology, University of California San Diego, USA. spond@ucsd.edu

Molecular Biology and Evolution
|July 5, 2006
PubMed
Summary

Phylogenetic analysis struggles with homologous sequences due to recombination. This study introduces a new framework using genetic algorithms to identify recombination break points, improving evolutionary sequence analysis.

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Area of Science:

  • Computational Biology
  • Evolutionary Genetics
  • Bioinformatics

Background:

  • Phylogenetic trees are insufficient for modeling homologous sequence evolution influenced by recombination or gene conversion.
  • Ignoring phylogenetic incongruity can lead to failures in sequence analysis methods, such as detecting non-neutral evolution.

Purpose of the Study:

  • To develop a model-based framework for analyzing homologous sequences with recombination.
  • To identify recombination break points and involved sequences within multiple sequence alignments.
  • To enable accurate evolutionary analysis of sequences affected by recombination.

Main Methods:

  • Utilizes a genetic algorithm to search multiple sequence alignments for recombination break points.
  • Quantifies statistical support for the identified break point locations.

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  • Identifies specific sequences or clades implicated in recombination events.

    • Main Results:

    • The proposed framework effectively identifies putative recombination break points and associated sequences.
    • The method is computationally efficient and scalable for distributed environments.
    • Performance validated on simulated and benchmark datasets.

    Conclusions:

    • The developed framework accurately models sequence evolution involving recombination.
    • Prescreening alignments with this method facilitates the analysis of recombinant sequences for positive selection.
    • This approach enhances the reliability of phylogenetic and evolutionary analyses.