easyLINKAGE

easyLINKAGE performs linkage analyses by integrating established linkage-analysis programs to conduct two-point and multi-point analyses, run simulations, and produce genome-wide and chromosomal postscript plots of LOD scores, NPL scores, and P-values for genetic mapping.

Key Features:

• Automated setup and execution: Automates preparation and execution of linkage analyses.
• Linkage analysis methods: Two-point analyses via FastLink v4.1 and SPLink v1.09, and multi-point analyses via GENEHUNTER v2.1 and GENEHUNTER-PLUS with the emendation by Kong and Cox v1.2.
• Simulation: Incorporates SLINK v2.65 for simulation of genetic data and assessment of linkage scenarios.
• Visualization: Generates genome-wide and chromosomal postscript plots of LOD scores, NPL scores, P-values, and other analysis parameters.

Scientific Applications:

• Genetic mapping: Identification and localization of genes associated with traits using LOD and NPL statistics.
• Complex inheritance studies: Analysis of multi-point linkage to investigate complex hereditary patterns.
• Result validation: Use of SLINK-based simulations to validate linkage results and assess power under specified models.

Methodology:

Integration of established linkage-analysis programs (FastLink v4.1, SPLink v1.09, GENEHUNTER v2.1, GENEHUNTER-PLUS with the emendation by Kong and Cox v1.2, SLINK v2.65) to perform two-point and multi-point analyses, run simulations, and generate genome-wide and chromosomal postscript plots of LOD scores, NPL scores, and P-values.