Table 2.

Naive co-occurrence measures differ in how they score ineage-specific genes. With pairs of identical profiles over 30 species both Hamming distance and Pearson correlation constantly yield scores that indicate high similarity. In contrast, Fisher's exact test (two-tailed) and mutual information yield less significance with a narrower and broader than 50% species distributions.

presences	Hamming	Pearson	Fisher	mutual information
0/30	0	—	1	0
3/30	0	1	0.02	0.7
15/30	0	1	0.008	1
27/30	0	1	0.02	0.7
30/30	0	—	1	0