 # Compute probability and exit.
:test

 # Sequence data for the three partitions.
:align dna1.fasta
:align rna.fasta
:align dna2.fasta

 # Link the first and third partitions
:smodel 1,3:tn93+>Rates.free(n=3)

 # The second partition has a fixed alignment.
:smodel 2:tn93
:imodel 2:none

 # Link the first and third partitions
:scale 1,3:
