Effect of cutoffs on a sample genome tree. First, for each query genome any genomes that are too distant to the query genome or too closely related to each other are removed (dotted lines) A). Second, we ensure that at least one genome (bold line) is close enough so that the GIs we identify were inserted from similar time frames and are not biased by the genomes that are currently available B). Also, we require that at least one genome is distant enough from the query genome (bold line) to ensure that the backbone sequences we identify were not inserted recently C). Finally, we require that there be a minimum of 3 reference genomes that have met all other criteria D). The reference genomes that have passed all the cutoffs are used for comparison with the query genome.