The EM algorithm was used for estimating relatedness with computation time proportioned to MN2, where M is the number of markers and N is the number of individuals. We implemented the method by using R-2.5.0. In the case of the CEPH data (91 individuals), computation times on a linux AMD Opteron 1.8GHz computer were 804.41 sec for 500 markers, 1617.68 sec for 1,000 markers and 7712.80 sec (2.14 hrs) for 5,000 markers.
