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

A nonparametric method for accommodating and testing across-site rate variation.

John P Huelsenbeck1, Marc A Suchard

  • 1Department of Integrative Biology, University of California, Berkeley, CA 94720, USA. johnh@berkeley.edu

Systematic Biology
|December 14, 2007
PubMed
Summary
This summary is machine-generated.

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

Smoothly Time-Varying Continuous Time Markov Chains in Phylogenetics.

ArXiv·2026
Same author

Reconciling fast Hepatitis B evolutionary rates with ancient co-divergence.

bioRxiv : the preprint server for biology·2026
Same author

Heterogeneity of Treatment Effects Across Nine Glucose-Lowering Drug Classes in Type 2 Diabetes: Extension of the LEGEND-T2DM Network Study.

Diabetes, obesity & metabolism·2026
Same author

Semaglutide and Neovascular Age-Related Macular Degeneration Among Adults with Type 2 Diabetes: An OHDSI Network Study.

Ophthalmology·2026
Same author

Global approaches to infectious disease surveillance and modeling.

Nature medicine·2026
Same author

Multimodal prediction of visual improvement in diabetic macular edema using real-world electronic health records and optical coherence tomography images.

medRxiv : the preprint server for health sciences·2026
Same journal

Diversification dynamics in the global radiation of gobies.

Systematic biology·2026
Same journal

Correction to: nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models.

Systematic biology·2026
Same journal

Phylogenomic challenges in polyploid-rich lineages: Insights from paralog processing and reticulation methods using the complex genus Packera (Asteraceae: Senecioneae).

Systematic biology·2026
Same journal

An evolving view of phylogenetic biogeography.

Systematic biology·2026
Same journal

Modeling Site-and-Branch-Heterogeneity with GFmix.

Systematic biology·2026
Same journal

Coalescent-based branch length estimation improves dating of species trees.

Systematic biology·2026
See all related articles

This study introduces a new Dirichlet process prior model to better account for across-site rate variation in phylogenetic analyses. This approach improves the accuracy of evolutionary models and phylogenetic estimates.

Area of Science:

  • Evolutionary Biology
  • Computational Biology
  • Phylogenetics

Background:

  • Substitution rates are fundamental to phylogenetic analysis, represented as branch lengths.
  • Variation in substitution rates across molecular sequence alignments is common due to functional constraints.
  • Ignoring across-site rate variation can lead to biased phylogenetic and model parameter estimates.

Purpose of the Study:

  • To develop and evaluate a novel model for across-site rate variation in phylogenetic analyses.
  • To improve the accuracy of phylogenetic inference by better accommodating rate heterogeneity.
  • To explore a new method for partitioning sites into rate classes using a Dirichlet process prior.

Main Methods:

  • A Dirichlet process prior was used to model rate partitioning across alignment sites.

Related Experiment Videos

  • This approach treats the partitioning scheme as a random variable, not a fixed assumption.
  • Markov chain Monte Carlo (MCMC) procedures were employed to sample rate partitions.

    • Main Results:

    • The Dirichlet process prior model demonstrated a better fit to DNA sequence alignments compared to traditional models.
    • The model identified underlying codon structure in protein-coding genes.
    • Sampled rate partitions showed closer resemblance to codon position-based partitioning than random partitions.

    Conclusions:

    • The Dirichlet process prior offers a more accurate and flexible approach to modeling across-site rate variation.
    • This method enhances phylogenetic analyses by better capturing rate heterogeneity and gene structure.
    • The findings suggest improved phylogenetic accuracy and parameter estimation in molecular sequence analysis.