Algorithm experimentation: Simulated data.

The first block of results shows the output of thread when run on the true IBD segments from Ped-sim. The second block of results shows setting A of the strong groups criteria, which requires more IBD support for individuals in ancient generations (described in more detail the main text). Similarly, the third block of results shows setting B, which requires more IBD support but relaxes the length requirements for older generations. The third column shows the number of unique IBDs (called by GERMLINE in the second two blocks). The fourth column shows how many iterations the algorithm needed to converge. The fifth column shows the number of ancestral (ungenotyped) individuals we were able to successfully reconstruct. The last column shows the average sequence similarity of the individuals we were able to reconstruct, as compared to their true genomes.
(XLSX)