I am attempting to analyse the evolution of a gene superfamily and
have a couple of queries which I hope someone out there can answer.
My main worry is the selection of outgroup sequences;
Should one attempt to generate an 'ancestral sequence' from the
known sequences. However, this may lead to bias since some sequences may
be over represented due to closely related sequences in sub families.
Use sequences from Drosophila or other invertebrate were there has
not been a large amplification since these may best corrospond to the
'original gene' or at least a rough approximation of the ancestral
sequence. This seems the most appropriate to me.
Simply use the most divergent sequence. This seems the most
obvious answer but strikes me as being the least appropriate.
Any comments and suggestions will be gratefully received.
Dr Keith Sutton
Reproductive Medicine Laboratory
University of Edinburgh