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Related Experiment Videos

Direct optimization, affine gap costs, and node stability.

Lone Aagesen1

  • 1Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024-5192, USA. laagesen@darwin.edu.ar

Molecular Phylogenetics and Evolution
|June 7, 2005
PubMed
Summary

Combining DNA data partitions enhances phylogenetic analysis robustness. Phylogenetic trees remain more consistent across alignment parameter costs when data partitions are combined, especially with affine gap costs.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Evolution

Background:

  • Phylogenetic analysis relies on DNA sequence homology assignment.
  • Alignment parameter costs significantly influence phylogenetic outcomes.
  • Dataset robustness to parameter cost variations is crucial for reliable conclusions.

Purpose of the Study:

  • To investigate node stability in phylogenetic analyses.
  • To compare separate versus combined data partition analyses.
  • To assess robustness to alignment parameter cost changes.

Main Methods:

  • Explored node stability across different cost sets.
  • Measured robustness by successive parameter changes before clade loss.
  • Included base change costs, gap penalties, and affine gap costs.

Related Experiment Videos

  • Analyzed three datasets with multiple data partitions.

    • Main Results:

    • Combining data partitions did not significantly increase the number of clades across the parameter space.
    • Trees from combined partitions with affine gap costs showed higher similarity than those without.
    • Combined analyses with affine gap costs demonstrated greater robustness, with ~80% of clades resisting parameter changes.

    Conclusions:

    • Combining data partitions improves phylogenetic tree consistency, particularly when using affine gap costs.
    • Robustness to alignment parameter costs is enhanced through data partition combination.
    • Phylogenetic results are more reliable when diverse data partitions are integrated and analyzed cohesively.