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Re: Rconstructing DNA (was Re: Dino-fuzz found in amber?)
I see two possibilities:
1) Reconstruct the DNA sequence to exactly the level of detail you can
guarantee, and no further. The sequence will contain lots of those extra
symbols like R and Y. Deal with it.
2) Don't reconstruct the DNA sequence. Use the aa sequence directly for
phylogenetic analysis. That's actually done fairly often even when the
DNA sequence is known.