I do not get an error when I run it.
A simpler approach (that avoids the nested loops and the if block):
Ai = mat == 'A'; % Logical Index
Ci = mat == 'C'; % Logical Index
Ti = mat == 'T'; % Logical Index
Gi = mat == 'G'; % Logical Index
Ant_Simpl_Mat = zeros(size(mat)); % Preallocate Output Matrix
Ant_Simpl_Mat(Ai) = 'T'; % Substitute
Ant_Simpl_Mat(Ci) = 'G'; % Substitute
Ant_Simpl_Mat(Ti) = 'A'; % Substitute
Ant_Simpl_Mat(Gi) = 'C'; % Substitute
Ant_Simpl_Mat = char(Ant_Simpl_Mat) % Convert To ‘char’
It produces the same result as your code with my test matrix, so I assume both are correct.
