QM-QXM is a C program that performs single-SNP, quantitative trait association testing for the autosomal chromosomes and the X-chromsome in samples with known relatedness. Kinship coefficients (and inbreeding coefficients for inbred pedigrees) are required to run the QM-QXM program. Two software programs that can be used to obtain autosomal and X-chromosome kinship and inbreeding coefficients are:

(1) The KinInbcoef software of Catherine Bourgain and Qian Zhang. The output file of the KinInbcoef program has the exact format required for the MQLS-XM software.

and

(2) The KinInbcoefX software of Qian Zhang, Catherine Bourgain, and Mary Sara McPeek. The output file of the KinInbcoefX program has the exact format required for the MQLS-XM software.



The Format_Ped_Pheno software of Timothy Thornton and Mary Sara McPeek can be used to to relabel all the families and the individuals in a pedigree/phenotype information file so that the family IDs and individual IDs conform to the requirements of the MQLS-XM, KinInbcoef and KinInbcoefX software. This program takes as input a pedigree/phenotype information file and outputs files that are in the required formats for the three software packages.

Acknowledgments: We gratefully acknowledge Jerry Halpern (funn@stanford.edu) for his contribution to the programming.