Statistical Genetics and Genomics Software

These are software that I have used or studied at one point. There is no particular order.

Linkage Analysis

PANGAEA: Pedigree Analysis for Genetics (and Epidemiological Attributes), including MORGAN and Pedfiddler.
Loki uses a Bayesian MCMC algorithm to do combined segregation and linkage analyses on complex pedigrees with quantitative traits (notes)
Genehunter: exact model-based and model-free linkage analyis using (improved) Lander-Green algorithm. Related links: Web-Genehunter, Parallel Genehunter, Genehunter Plus.
Solar (notes)
Merlin (notes)

FBAT (notes): family-based asssociation tests
Haploview: haplotype viewer and analysis tool.
PHASE: aplotype reconstruction, and recombination rate estimation from population data.
SNPHAP: haplotyping by EM algorithm with some improvements.
haplo.stats: GLM with score tests using unphased genotypes, successor of haplo.score.
QTDT: Family based tests of linkage disequilibrium for quantitative traits.
Hplus
hapstat
Chaplin: case-control haplotype inference package.
GenABEL: R library for Genome-wide association analysis.
Genetic Power Calculator
GWAS

Structure: using multi-locus genotype data to investigate population structure.
LAMARC: likelihood analysis with Metropolis algorithm using random coalescence.
SIMCOAL 2.0: a coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models.
Richard Hudson's programs: ms and two-locus
LDhat: estimating recombination rates and hotspots.

R Packages
SAM: Supervised learning software for genomic expression data mining.
GenMAPP: visualize gene expression data on maps representing biological pathways and groupings of genes.