CoCoa

The program CoCoa is a free software package for estimating the coefficient of coancestry from multilocus genotype data. The symmetric matrix that is obtained by estimating the coefficient of coancestry for all pairwise combinations of the genotyped individuals, can be used to model the covariance structure of genetic background effects. This is particularly useful when a linear mixed model is applied to analyse phenotypical data that originates from breeding programs or association studies. Depending on the estimator, CoCoa can handle most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs. The manual gives an overview of the available coancestry measures that can be estimated using CoCoa. Besides coancestry estimation, CoCoa also provides several useful matrix manipulation tools such as matrix bending, bounding and inversion. To allow the resulting matrices to be used in the variance structure of a linear mixed model, CoCoa can store matrices in various file formats, specific to the most commonly used linear mixed model packages.