Gonçalo's Software
The following software packages can be downloaded freely. If you find them useful, please fill out the accompanying registration form and cite them in your work.
Merlin	Fast pedigree analyses, including non-parametric linkage, error detection and haplotyping.
LAMP	Powerful parametric tests of association for pedigree and case-control data, that provide an alternative to standard approaches based on transmission disequilibrium. Can also be used to maximize LOD scores over mode of inheritance.
MACH	Rapid high-quality haplotyping and genotype inference. Currently in beta release.
QTDT	Linkage disequilibrium and association analyses for quantitative traits.
GOLD	A graphical package for the overview of linkage disequilibrium.
PedStats	A utility for summarizing the contents of pedigree files with the ability to produce graphical output in PDF format.
GRR	A graphical tool for identifying relationship errors in genome scan data.
CaTS	Graphical power calculator for case-control association studies, including two stage studies.
GAS	Graphical web interface for one-stage association studies. Adapted from CaTS algorithms.
Metal	Meta-Analysis Tool for genome-wide association scans.
FUGUE	Haplotype frequency estimation in families and unrelated individuals.
Pseudo	This is a companion tool for Merlin that facilitates gene-dropping simulations. In addition to calculating summary statistics for standard gene-dropping simulations, Pseudo can read in simulated LOD scores for individual families and shuffle them to create a series of "Pseudo" replicates.
Additional code.
SNP-HWE	Routines for exact SNP tests of Hardy-Weinberg Equilibrium.