Re: The shape of inbreeding/outbreeding depression

> From: Guy Hoelzer <hoelzer@xxxxxxx>
> Assuming these sequences are properly aligned to ensure the homology
> between opposed letters, the sequence similarity between these two
> sequences is 0% because none of the opposed letters are the same.

I don't believe anyone of reasonable intelligence would make such a
stupid assumption, so you seem to be creating a strawman to knock down,
so your hypothetical calculation is worthless.

> I think my calculation is clear from my statement, although it only
> required scanning the sequences and counting similarities.

It's not clear at all what algorithm you use to count what matches as
opposed to what doesn't match, given the cost of rearranging one or the
other genome sequence to make it match the other. Is that cost zero,
whereby any shuffling whatsoever of some mix of the four bases would
count as identical to the original, or is that cost infinity, whereby
if there's a single rearrangement then the similarity is considered to
be zero as you strawman-calculated above? Since you refuse to put a
number on the cost of rearrnaging to achieve alighment, there's no
point discussing such matters with you. Your method is non-defined.

.

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