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

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.

Heiko A Schmidt1, Korbinian Strimmer, Martin Vingron

  • 1Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, D-14195 Berlin, Germany. hschmidt@eva.mpg.de

Bioinformatics (Oxford, England)
|April 6, 2002
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

CAdir: Joint clustering of cells and genes for single-cell transcriptomics with visualization-driven cluster quality assessment.

PLoS computational biology·2026
Same author

Integrative multi-omics analysis of growth plate regulation underlying body size in miniature pigs.

Communications biology·2026
Same author

Modeling strategies for <i>in vivo</i> transcription factor binding predictions.

Bioinformatics advances·2026
Same author

Genomic GC bias correction improves species abundance estimation from metagenomic data.

Nature communications·2025
Same author

GTestimate: improving relative gene expression estimation in scRNA-seq using the Good-Turing estimator.

GigaScience·2025
Same author

Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus.

Nature structural & molecular biology·2025
Same journal

Biomedical Concept Recognition with Error-aware Negative-enhanced Ranking Framework.

Bioinformatics (Oxford, England)·2026
Same journal

TEDLH: Domain HMMs for sensitive detection of remote homologues.

Bioinformatics (Oxford, England)·2026
Same journal

PLNFGL: Joint Estimation of Multi-Condition Gene Networks from Single-cell RNA-seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026
See all related articles

TREE-PUZZLE is a powerful software package for phylogenetic analysis using DNA and protein sequences. Its tree reconstruction is now parallelized for faster analysis of large datasets.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Evolutionary Biology

Background:

  • TREE-PUZZLE is a software package for quartet-based maximum-likelihood phylogenetic analysis.
  • It offers methods for reconstructing, comparing, and testing phylogenetic trees and models.
  • The software supports both DNA and protein sequence data.

Purpose of the Study:

  • To enhance the performance of phylogenetic analyses for large datasets.
  • To provide a parallelized version of the tree reconstruction module.
  • To improve the efficiency of phylogenetic tree and model analysis.

Main Methods:

  • Parallelization of the tree reconstruction module using message passing.
  • Implementation on clusters of workstations and parallel computers.

Related Experiment Videos

  • Development in ANSI C for broad system compatibility.

    • Main Results:

    • Reduced waiting time for phylogenetic analyses on larger datasets.
    • Successful parallelization of the tree reconstruction process.
    • Enhanced computational efficiency for phylogenetic studies.

    Conclusions:

    • TREE-PUZZLE provides an efficient and parallelized approach to phylogenetic analysis.
    • The software is versatile, supporting DNA and protein sequences across multiple operating systems.
    • It is a valuable tool for researchers in evolutionary biology and bioinformatics.