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src/b/i/biopython-1.63/Bio/Nexus/Nexus.py   biopython(Download)
            elif self.datatype == 'protein':
                #TODO - Should this not be ExtendedIUPACProtein?
                self.alphabet = IUPAC.IUPACProtein() # fresh instance
                self.ambiguous_values = {'B':'DN', 'Z':'EQ', 'X':IUPACData.protein_letters}
                # that's how PAUP handles it

src/b/i/biopython-HEAD/Bio/Nexus/Nexus.py   biopython(Download)
            elif self.datatype == 'protein':
                #TODO - Should this not be ExtendedIUPACProtein?
                self.alphabet = IUPAC.IUPACProtein() # fresh instance
                self.ambiguous_values = {'B':'DN', 'Z':'EQ', 'X':IUPACData.protein_letters}
                # that's how PAUP handles it