LDWeaver

LDWeaver identifies pairs of genetic variants exhibiting unusual linkage disequilibrium in bacterial genomes to detect co-selection or epistasis using sequence alignments in FASTA and reference annotations in GenBank or GFF formats.

Key Features:

• Exhaustive GWES Analysis: Performs genome-wide epistasis and co-selection (GWES) analysis across both short- and long-range LD to detect interactions within genes, promoter regions, and operons.
• Hypothesis Generation: Leverages large genomic surveys of major human bacterial pathogens to generate hypotheses about co-selection, with validation through functional annotation and phenotypic measurements.
• Statistical Significance Ranking: Employs approximate statistical significance to rank outlier LD links for prioritization of candidate interactions.
• Comprehensive Output: Reports results in TSV format accompanied by annotations and figures describing identified LD pairs.
• Facilitation of Bacterial Evolution Studies: Integrates GWAS with GWES analyses to provide a phenotype-free approach for hypothesizing selective processes affecting multiple loci.

Scientific Applications:

• Bacterial evolution studies: Dissects co-selection and epistasis to study adaptive processes in bacterial populations.
• Genetic architecture analysis: Characterizes complex LD patterns within genes, promoters, operons, and across genomic distances.
• Population-genomic hypothesis generation: Produces testable hypotheses from large-scale surveys of human bacterial pathogens.
• Complementing GWAS: Provides phenotype-free insights into selective processes and multi-locus interactions that complement GWAS findings.

Methodology:

Accepts FASTA alignments and GenBank or GFF annotations, performs exhaustive GWES across short- and long-range LD to identify high-LD variant pairs, ranks outlier links using approximate statistical significance, and outputs results in TSV with annotations and figures.