LDhelmet

LDhelmet is a software package used in population genetics to infer fine-scale recombination rates along a genome from patterns of genetic variation. It analyzes linkage disequilibrium in DNA sequence data to produce a recombination map, typically expressed as rho = 4N_e r, where N_e is the effective population size and r is the per-site recombination rate. The resulting map highlights how recombination intensity varies across genomic regions.

Methodology is based on coalescent theory and likelihood-based inference. LDhelmet builds on previous LD-based methods and uses a statistical model of recombination to estimate local rates. It precomputes likelihoods for a grid of recombination-rate values and then applies an optimization or sampling framework to infer the recombination rate across the genome. The output is a continuous or interval-based map of recombination intensity, together with uncertainty measures, suitable for downstream analyses.

Data requirements include population-level DNA sequence data, typically an alignment of haplotypes or unphased genotypes with SNP calls and genomic coordinates. Users may specify a mutation model and certain demographic assumptions; the method is designed to be robust to moderate deviations from simple demographic histories. Proper data preparation and quality control are important for reliable inferences.

Output and applications involve a genome-wide recombination-rate map with associated confidence estimates. LDhelmet maps are used to explore recombination landscapes, compare rates across populations or species, and inform studies in evolutionary biology, demographic history, and genome organization.

Availability and implementation notes: LDhelmet is open-source software implemented in C and designed to run on Linux systems. It is distributed with documentation, example datasets, and tutorials to guide researchers in applying the method to their sequencing data.