User:Dbeatty/Sandbox

Association Mapping (or LD Mapping )

Background

Population structure can lead to false positives. GC - Gas Chromotography

Affeymetrix LD (C/C++)
FASTLINK (C - last updated 1999?)
Software for Linkage and Mapping
PyPop (Python/C)
Haploview (Java)
Software from Broad Institute (that may or may not be helpful)
MERLIN (Linkage, Parametric Linkage, IBD Estimation, Regression, LD, Association Analysis) (C++)
LAMP (Linkage and Association Modeling in Pedigrees - uses maximum likelihood model) (C++)
All Software from BIO 666
Association Mapping Software (including MCMC, HapCluster, and Block-Association Mapping)
SPAGeDi (Spatial Pattern Analysis of Genetic Diversity - primarily designed to characterize the spatial genetic structure of mapped individuals and/or mapped populations using genotype data of any ploidy level.)
TASSEL (is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.)
Structure (is a free software package for using multi-locus genotype data to investigate population structure.)
STRAT (is a companion program to structure. It is written for use in association mapping, enabling valid case-control studies even in the presence of population structure.)
Links to software from STATISTICAL GENETICS: Gene Mapping Through Linkage and Association textbook

correlation coefficient delta (Hill and Robertson 1968)
Lewontin's D' (range constrained by allele frequencies 1964)
robust formulation of the population attributable risk delta
Yule's Q
Kaplan and Weir's proportional difference d under the assumption of complete disequalibrium between disease and marker loci