Yun Li's Software
The following software packages can be downloaded freely. If you find them useful, please email me: yunli@med.unc.edu. Comments and suggestions are welcome!
CalcMatch	Concordance between two sets of genotype data (wiki) (source)
Concatenate Haplotypes	Concatenate Two Sets of Haplotypes
doseR2	Dosage r2 Calculator
ExtractImputed	Extract information for a subset of sites from imputed dataset
haploxt	LD Calculator from Phased Haplotypes (wiki)
KARMA	K-tuple Alignment with Rapid Matching Algorithm
Ligate Haplotypes	Ligate Haplotypes with Overlapping
MaCH	MArkov Chain Haplotyping: rapid haplotyping, genotype imputation from genotype or resequence data (wiki)
MaCH-Admix	MArkov Chain Haplotyping for Admixed Populations
mach2dat	Imputation-based analysis of binary traits (windows version)
mach2qtl	Imputation-based analysis of quantitative traits
prob2plink	Converts MaCH prob+info output to PLINK dosage file
r2_hat	Calculate Imputation Quality Estimate (r2_hat) from dosage data
RegionalHapMapExtractor	Extract a Candidate Region from HapMap phase 1+2 for MaCH imputation
splitPed	Splits a pedigree file into smaller files with subsets of markers (wiki)
splitRef	Splits a reference haplotype file into smaller files with subsets of markers (wiki)
thunder	LD-based genotype caller and haplotyper on massively parallel sequencing data (wiki)
WHaIT	Weighted Haplotype and Imputation dosage Tests for multiple rare variants
Other
Goncalo Abecasis's Extractor	Filter a file by exactly matching key word in the first column
Liming Liang's MQLS	Imputation-based analysis of binary traits for family data without covariates
Goncalo Abecasis's new_fugue	LD and Frequency Calculator