PedPeel

PedPeel computes optimal peeling orders for zero-loop pedigrees with incomplete genotypic information to minimize computational complexity during likelihood calculations for linkage analysis and genetic parameter estimation.

Key Features:

• Optimal Peeling Order: Uses a graph-theoretic algorithm to determine an optimal peeling order for zero-loop pedigrees with incomplete genotypes, minimizing the number of likelihood calculations required.
• Handling Complex Pedigrees: Specifically tailored to zero-loop pedigrees where traditional approaches may struggle to find efficient peeling orders, thereby reducing computational burden in linkage analysis.
• Integration with Existing Software: Compatible with software that uses the Elston–Stewart algorithm for likelihood calculations, enabling use of optimized peeling orders within Elston–Stewart evaluations.

Scientific Applications:

• Linkage Analysis: Facilitates testing for linkage across multiple marker loci by reducing computational demands for likelihood-based analyses.
• Genetic Parameter Estimation: Improves computational feasibility of precise estimation of genetic parameters in family-based studies with incomplete genotypes.
• Large Family Pedigree Analysis: Supports analysis of large family datasets with complex zero-loop pedigrees by reducing computational inefficiencies.

Methodology:

A graph-theoretic algorithm systematically selects the most efficient peeling order for zero-loop pedigrees with incomplete genotypic data to minimize the number of likelihood calculations.