Sometimes you don't want it to be just a label. Say you want to compare fitness of two closely related organisms that reproduce sexually - then you don't want them to inter-breed.
Yes, this is true. But there should be a standard way to do that, instead of just making things work the wrong way because sometimes it is useful. Another way would be to simply program your creatures to ingoe each other as partners (risky) or mess up their dna - if they have ND execution, for example, you can completely invert the order of their genes without changing their functionality: and they will never be able to interbreed.
They are using the best software available and thier alignments usually take overnight and sometimes go for several days. Which makes me think that any program that does this in a fraction of a second is a sham.
It may be so. Or it may be that your colleagues work on much bigger data collections that we need to do. I don't think that aligning similar parts should be (nor that it can be) an error free procedure. It should only make things work better than they do now.
Basically, if you can do it - great! I won't complain. But I don't see why UID system can't be implemented - it is very powerful and yet it is very easy to add...
I prefer my system, which is not very different from yours except for the fact that
1) it doesn't need explicit and arbitrary marking of the code
2) it works _preferably_ (but not necessarily) on entire genes.
3) it's straightforward to implement
