Mostly for Mungo: I just ran across another example for JAL-845:
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001994
(about nucleotide drift in protein families)
The corrigenda has the note on where to find the ancestral sequences.
A followup example is here (data may be not so easily accessible):
http://www.nature.com/nature/journal/v512/n7513/full/nature13410.html
Also - the package I was thinking of that we should look at about propagating nucleotide consensus to protein (JAL-1681) is MACSE.. but I looked at the paper, and it doesn't actually do what we are thinking of doing 
j.
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Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, College of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
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