Tree topology and fingerprint (distributions of BLAST hit weights) of tests on simulated genomes. One representative test using either the idealized tree topology (A) or the randomized tree topology (B) is depicted (see text). The kernel density function of close weight distribution for both topologies (C, D) shows the distribution of all genes in the input genomes in black, and that of actual positive genes (derived from HGT events from distal group to self group) in red. Genes involved in other simulated evolutionary events are shown in different colors in the lower panels. Locations of these genes in the general distribution are indicated as a rug below each plot. The scales of x-axes between the upper and the lower panels are identical. Cutoffs computed by the program distinguishing the atypical region from the typical region are represented in dashed (for relaxed criterion) and dotted (for conservative criterion) lines.