ArticleG3 (Bethesda, Md.)2023
GWLD: an R package for genome-wide linkage disequilibrium analysis.
Article in G3 (Bethesda, Md.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- The heterozygous pineapple genome demonstrates the importance of haplotype-resolved plant genomes.Horticulture research · 2026Article
- Identification of SNPs Associated With mRNA Expression Differences of the Complement Receptor Type 1-Like Gene in Landrace Weaned Piglets.Veterinary medicine and science · 2026Article
- Climate-induced patterns of activity and nest conditions select for genes associated with growth and maturation in a widespread lizard species.Research square · 2026Article
- Investigating genetic differentiation between brackish and fresh water collections of the arboviral vector Aedes aegypti.Parasites & vectors · 2026Article
- Unraveling the genetic architecture of anti-nutritional factors in soybean (Glycine max.) for nutritional enhancement.Scientific reports · 2025Article
- Local adaptation to climate has facilitated the global invasion of cheatgrass.Nature communications · 2025Article
- Unraveling Evolution in the Homoploid Complex ofEcology and evolution · 2025Article
- NXPE1 alters the sialoglycome by acetylating sialic acids in the human colon.Nature communications · 2025Article
- Unveiling host-genetic drivers of caecal microbial communities in chickens through genome-wide association studies.Frontiers in microbiomes · 2025Article
- Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Linkage disequilibrium (LD) analysis is fundamental to the investigation of the genetic architecture of complex traits (e.g. human disease, animal and plant breeding) and population structure and evolution dynamics. However, until now, studies primarily focus on LD status between genetic variants located on the same chromosome. Moreover, genome (re)sequencing produces unprecedented numbers of genetic variants, and fast LD computation becomes a challenge. Here, we have developed GWLD, a parallelized and generalized tool designed for the rapid genome-wide calculation of LD values, including conventional D/D', r2, and (reduced) mutual information (MI and RMI) measures. LD between genetic variants within and across chromosomes can be rapidly computed and visualized in either an R package or a standalone C++ software package. To evaluate the accuracy and speed of LD calculation, we conducted comparisons using 4 real datasets. Interchromosomal LD patterns observed potentially reflect levels of selection intensity across different species. Both versions of GWLD, the R package (https://github.com/Rong-Zh/GWLD/GWLD-R) and the standalone C++ software (https://github.com/Rong-Zh/GWLD/GWLD-C++), are freely available on GitHub.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.