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

Integer linear programming as a tool for constructing trees from quartet data.

Jan Weyer-Menkhoff1, Claudine Devauchelle, Alex Grossmann

  • 1Universität Göttingen, Biologische Fakultäet, Institut für Mikrobiologie und Genetik, Abt. Bioinformatik Goldschmidtstr. 1, D-37073 Göttingen, Germany. jan@gobics.de

Computational Biology and Chemistry
|June 28, 2005
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

A genome-wide association study of facial morphology identifies novel genetic loci in Han Chinese.

Journal of genetics and genomics = Yi chuan xue bao·2021
Same author

Statistical testing and power analysis for brain-wide association study.

Medical image analysis·2018
Same author

Reconstructing Unrooted Phylogenetic Trees from Symbolic Ternary Metrics.

Bulletin of mathematical biology·2018
Same author

Comprehensive transcriptome analysis of neocortical layers in humans, chimpanzees and macaques.

Nature neuroscience·2017
Same author

Sequence, structure and ligand binding evolution of rhodopsin-like G protein-coupled receptors: a crystal structure-based phylogenetic analysis.

PloS one·2015
Same author

Quartet-based methods to reconstruct phylogenetic networks.

BMC systems biology·2014
Same journal

Integrative in silico analysis identifies functionally and regulatively relevant nsSNPs in the TRIB3 gene.

Computational biology and chemistry·2026
Same journal

MARS: Multi-anchor reasoning for reliable toxicity prediction under distribution shift.

Computational biology and chemistry·2026
Same journal

Zadeh-based fuzzy analysis of carreau tri-hybrid nanofluid hemodynamics in a straight artery with irregular triangular stenosis.

Computational biology and chemistry·2026
Same journal

Exploring C<sub>6</sub>N<sub>6</sub> as an effective drug delivery carrier for anticancer drugs mercaptopurine and thiotepa: A DFT and MD approach.

Computational biology and chemistry·2026
Same journal

Role of Artificial Intelligence in bioinformatics: Revolutionizing molecular docking and DNA tokenization.

Computational biology and chemistry·2026
Same journal

An interpretable framework for cancer drug response prediction using integrated drug and multi-omics data with a hybrid Bi-LSTM-GRU network.

Computational biology and chemistry·2026
See all related articles

This study introduces an integer linear programming method to solve the quartet puzzling problem, finding optimal binary X-trees from confidence values. The approach uses rate-matrix diagonals for accurate phylogenetic tree reconstruction.

Area of Science:

  • Phylogenetics and Computational Biology

Background:

  • The quartet puzzling problem aims to reconstruct phylogenetic trees by analyzing quartets (sets of four taxa).
  • Accurate phylogenetic tree reconstruction is crucial for understanding evolutionary relationships.

Purpose of the Study:

  • To develop an exact method for solving the quartet puzzling problem using integer linear programming.
  • To propose a novel method for generating confidence values for quartet trees from biological sequence data.

Main Methods:

  • Integer linear programming formulation for the quartet puzzling problem.
  • Calculation of confidence values using inner products of rate-matrix diagonals from taxon pairs.
  • Application to mammalian mitochondrial sequence data.

Main Results:

Related Experiment Videos

  • An exact solution for the quartet puzzling problem was achieved via integer linear programming.
  • A new method for deriving quartet tree confidence values was successfully applied.
  • Phylogenetic trees were reconstructed for mammalian mitochondrial sequences.

Conclusions:

  • Integer linear programming provides an effective method for solving the quartet puzzling problem.
  • The proposed method for generating confidence values is a viable approach for phylogenetic analysis.
  • The methodology is applicable to large biological datasets for evolutionary studies.