Babelomics set of tools for Single Nucleotide Polymorphisms (SNP) analysis can be found in the Genomic button of the Tools drop down menu.
This tool allows the study of SNPs applying microarray technology, and through two different analysis : Association Analysis based on SNPs and Genotype Stratification.
The basic association test is for a disease trait and is based on comparing allele frequencies between cases and controls (empirical p-values are available). Also implemented are the Chi-square case/control association test, Fisher's exact test, Linear, Logistic regression and TDT test (only for family-based analysis). As well some modifications are implemented as the SNP filtering on the basis of minor allele frequency.
Another study that one can handle with our tools is a simple but potentially powerful approach to population stratification. Complete linkage agglomerative clustering is applied, based on pairwise identity-by-state (IBS) distance. In addition, some modifications are taken into account in the clustering process: a significant pairwise population concordance test for whether two individuals belong to the same population (i.e. do not merge clusters that contain significantly different individuals) and also cluster size restrictions (i.e. such that, with a cluster size of 2, for example, the subsequent association test would implicitly match every case with its nearest control, as long as the case and control do not show evidence of belonging to different populations). *
( * taken from PLINK documentation in [[http://pngu.mgh.harvard.edu/~purcell/plink/]] )