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 Concept Videos

You might also read

Related Articles

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

Sort by
Same author

Evaluating the phylogenetic signal of morphosyntax.

Poznan studies in contemporary linguistics : PSiCL·2026
Same author

Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads.

Molecular biology and evolution·2025
Same author

Fast and accurate deep learning scans for signatures of natural selection in genomes using FASTER-NN.

Communications biology·2025
Same author

Scalable CNN-based classification of selective sweeps using derived allele frequencies.

Bioinformatics (Oxford, England)·2024
Same author

Comparative Genomics Uncovers the Evolutionary Dynamics of Detoxification and Insecticide Target Genes Across 11 Phlebotomine Sand Flies.

Genome biology and evolution·2024
Same author

Evolution of gene regulatory networks by means of selection and random genetic drift.

PeerJ·2024
Same journal

From Gene Copies to Cell Numbers: Advancing Quantitative Approaches in Protistan Ecology Using Digital PCR.

Molecular ecology resources·2026
Same journal

EasyCen: A Lightweight Framework for Centromere Localisation and Repeat-Organisation Profiling in Telomere-to-Telomere Genomes.

Molecular ecology resources·2026
Same journal

A Practical Framework for GT-Seq Panel Optimization.

Molecular ecology resources·2026
Same journal

Comparison of Environmental DNA and Bulk DNA Metabarcoding for Assessing Terrestrial Arthropod Diversity Across Three Habitat Types on Guam.

Molecular ecology resources·2026
Same journal

pr2-Wormifier: A Bioinformatics Pipeline to Create Custom Reference Databases for Improved Metabarcoding of Marine Protists.

Molecular ecology resources·2026
Same journal

Individual Identification of Prey in Carnivore Scats.

Molecular ecology resources·2026
See all related articles

Related Experiment Video

Updated: Nov 3, 2025

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae
07:55

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae

Published on: September 11, 2022

2.0K

quickLD: An efficient software for linkage disequilibrium analyses.

Charalampos Theodoris1, Tze Meng Low2, Pavlos Pavlidis3

  • 1Technical University of Crete, Chania, Greece.

Molecular Ecology Resources
|June 1, 2021
PubMed
Summary
This summary is machine-generated.

quickLD is a new open-source software for linkage disequilibrium (LD) analysis. It efficiently calculates LD across long distances, significantly speeding up genetic analyses on large datasets.

Keywords:
computer programhigh-performance softwarelinkage disequilibrium

More Related Videos

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

3.5K
Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
11:35

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

13.2K

Related Experiment Videos

Last Updated: Nov 3, 2025

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae
07:55

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae

Published on: September 11, 2022

2.0K
A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

3.5K
Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
11:35

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

13.2K

Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Traditional software for linkage disequilibrium (LD) analysis faces computational challenges with increasing genetic data size and distance between variants.
  • Existing tools often exhibit quadratic time and memory complexity, limiting scalability for large-scale genetic studies.
  • Current software underutilizes modern CPU and GPU computational power, hindering efficient analysis of thousands of samples.

Purpose of the Study:

  • To introduce quickLD, a novel, stand-alone, and open-source software designed for efficient linkage disequilibrium (LD) analysis.
  • To address the computational limitations of existing LD analysis tools, particularly for long-range variant interactions.
  • To enable faster and more memory-efficient computation of LD statistics, facilitating large-scale genetic research.

Main Methods:

  • quickLD computes pairwise LD statistics, including r², between genetic variants.
  • The software is optimized to handle calculations within single or arbitrarily distant genomic regions.
  • It leverages modern processor architectures, achieving high CPU and GPU performance utilization.

Main Results:

  • quickLD demonstrates negligible memory requirements, even for long-range LD calculations.
  • The software achieves up to 95% of theoretical CPU peak performance and 97% of GPU peak performance.
  • Processing speeds are 21.5x faster on multicore CPUs and 49.5x faster using combined CPU and GPU power compared to state-of-the-art methods.

Conclusions:

  • quickLD offers a significant computational advantage for linkage disequilibrium analysis, overcoming the limitations of existing tools.
  • Its efficiency and scalability make it suitable for large-scale genetic studies involving thousands of samples.
  • The software supports various population genetics analyses, including studies of selection, recombination, genetic drift, inbreeding, and gene flow.