File: ciliate.cod

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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%                                                                      %%%%%
%%%%%            Ciliate macronuclear genetic code definitions             %%%%%
%%%%%                                                                      %%%%%
%%%%%    Only exchanges compared to the standard code must be defined.     %%%%%
%%%%%                                                                      %%%%%
%%%%%      (The last codon of the list is used for backtranslations        %%%%%
%%%%%       from protein to DNA sequences---therefore the wobbles)         %%%%%
%%%%%                                                                      %%%%%
%%%%%                                                                      %%%%%
%%%%%    Activate these definitions for your alignment by the following    %%%%%
%%%%%    command in the texshade environment:                              %%%%%
%%%%%                                                                      %%%%%
%%%%%                         \geneticcode{ciliate}                        %%%%%
%%%%%                                                                      %%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\codon{Q}{TAA,TAG,UAA,UAG,YAR}