This command is used to specify pairs of nucleotides. For example, your data may be RNA sequences with a known secondary structure of stems and loops. Substitutions in nucleotides involved in a Watson-Crick pairing in stems are not strictly independent; a change in one changes the probability of a change in the partner. A solution to this problem is to expand the model around the pair of nucleotides in the stem. This command allows you to do this. The correct usage is:
pairs <NUC1>:<NUC2>, <NUC1>:<NUC2>,..., <NUC1>:<NUC2>;
For example,
pairs 30:56, 31:55, 32:54, 33:53, 34:52, 35:51, 36:50;
specifies pairings between nucleotides 30 and 56, 31 and 55, etc. Only nucleotide data (DNA or RNA) may be paired using this command. Note that in order for the program to actually implement a "doublet" model involving a 16 X 16 rate matrix, you must specify that the structure of the model is 16 X 16 using "lset nucmodel=doublet".