M. m. musculus x M. m. domesticus hybrid male sterility intercross
R/qtl input files for the M. m. musculus x M. m. domesticus hybrid male sterility intercross MusculusxDomesticusF2Males_Rqtl_Input.csv.
The map file MusculusxDomesticus_MapFile.csv includes male and female animals to estimate the genetic map.
The F2 intercross file contains phenotype and genotype data for all males.
Reference: White et al. (2011), Genetics, 189: 289-304.

Wellcome Trust Concordance Analysis
Sequence alignments of wild-derived inbred strains nexusAlignments.tgz.
Genomic positions (build 37) and posterior probabilities for loci autosomesPartitionPositions.tgz.

MARKSIM
A program that extends Hudson's ms by enabling users to simulate microsatellite data sets under a variety of mutational models. SNP, SNP haplotype, and SNPSTR data sets may also be generated using MARKSIM. Output data sets are formatted for immediate use in STRUCTURE or (in the case of SNPs) SMARTPCA analysis.
Reference: Haasl and Payseur (2011), Heredity, 106: 158-171.
Please download documentation pdf first, which includes installation instructions.
Download program here.

THESTIMATE
A program to estimate microsatellite theta based on the estimators detailed in Haasl and Payseur (2010) Mol.Biol.Evol., 27: 2702-2715.
Download here.