Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Bootstrap method of interior-branch test for phylogenetic trees

T Sitnikova1

  • 1Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA. tanya@imeg.bio.psu.edu

Molecular Biology and Evolution
|April 1, 1996
PubMed
Summary

The bootstrap test for phylogenetic tree branch lengths is reliable, even with varying substitution rates. A new correction method improves reliability for both bootstrap and standard tests in phylogenetic analysis.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Is the donut in front of the car? An electrophysiological study examining spatial reference frame processing.

Canadian journal of experimental psychology = Revue canadienne de psychologie experimentale·2001
Same author

Evolution of vertebrate immunoglobulin variable gene segments.

Current topics in microbiology and immunology·2000
Same author

A new method for characterizing replacement rate variation in molecular sequences. Application of the Fourier and wavelet models to Drosophila and mammalian proteins.

Genetics·2000
Same author

Coevolution of immunoglobulin heavy- and light-chain variable-region gene families.

Molecular biology and evolution·1998
Same author

Evolution of immunoglobulin kappa chain variable region genes in vertebrates.

Molecular biology and evolution·1998
Same author

Evolution by the birth-and-death process in multigene families of the vertebrate immune system.

Proceedings of the National Academy of Sciences of the United States of America·1997

Area of Science:

  • Computational Biology
  • Phylogenetics
  • Statistical Genetics

Background:

  • Phylogenetic trees are crucial for understanding evolutionary relationships.
  • Accurate estimation of interior branch lengths is essential for robust phylogenetic inference.
  • Existing statistical tests for branch lengths have limitations, especially with complex evolutionary models.

Purpose of the Study:

  • To statistically evaluate the performance of the bootstrap test for interior branch lengths.
  • To compare the bootstrap test with the standard interior-branch test.
  • To develop and assess a correction method for improving the reliability of phylogenetic tree topology tests.

Main Methods:

  • Computer simulations were employed to examine the statistical properties of both tests.

Related Experiment Videos

  • Tests were evaluated under the null hypothesis for predetermined and estimated tree topologies.
  • The impact of varying substitution rates among sites was investigated.

    • Main Results:

    • Both bootstrap and standard tests are reliable when branch length estimates follow a normal distribution.
    • The bootstrap test maintains reliability even with varying substitution rates, unlike the standard test.
    • A simple correction method enhances the reliability of both tests for estimated topologies.

    Conclusions:

    • The bootstrap test offers greater robustness for phylogenetic branch length estimation, particularly under complex evolutionary scenarios.
    • The developed correction method provides a simpler and effective way to improve the reliability of phylogenetic tree topology testing.
    • Both tests can become conservative with an increasing number of sequence groups in star-like phylogenetic trees.