When calculating the distance between two genomes, how does one treat disabled connections?
For example, consider the following genome:
| [1, 0.2, E] | [2, 0.1, D] | [3, 0.2, E] | [4, 0.15, E] | [5, 0.3, D] | [7, 0.25, D] | [8, 0.25, E] | [9, 0.1, E] | |
| [1, 0.2, E] | [2, 0.2, E] | [3, 0.1, E] | [6, 0.15, E] |
For $\overline{W}$, the weighted sum of common genes, do I only sum the genes that are enabled in both (1 and 3), or do I sum all of the common genes (1, 2, and 3)?
For $D$, the disjoint genes, do I only count the disjoint enabled genes (4 and 6), or do I count all of them (4, 5, and 6)?
For $E$, the excess genes, do I only count the enabled genes (8 and 9), or do I count all of them (7, 8, and 9)?
And finally, for $N$, do I count all of the genes in the larger genome or just the enabled ones?
Oh, one last question. Is gene 2 now considered disjoint since it is disabled in the first genome?
