3 programs were used to analyze the DNA and determine the site(s) of mutation:
FinchTV
http://www.geospiza.com/Products/finchtv.shtml
http://www.genewiz.com/public/tools.aspx (for editing sequence)
BLASTX and BLASTn
http://blast.ncbi.nlm.nih.gov/Blast.cgi
Multalin
http://multalin.toulouse.inra.fr/multalin/multalin.html