We have had some requests from researchers at the Pasteur Institute in Dakar for applications, including :
MERLIN software developed at the University of Michigan, for linkage, association, pedigree analyses, haplotyping, etc
FBAT software developed at Harvard, for genetic association screening in Family-Based data design
PLINK software also developed at Harvard, most popular for GWAS study, including all the analysis pipeline.
If there are others, just reply to this topic.