 # Protect interleaved source, scalar command-line precedence, and additive repeated values.
 # This becomes obsolete if command files are replaced with a format that specifies merging itself.
:test

 # Keep model declarations before and after options, and ensure command-line scalars take precedence.
configBeforeOption = 1;
:tree ~Yule(taxa,1)

 # Sequence data for the three partitions.
:align dna1.fasta
:align rna.fasta
:align dna2.fasta
:alphabet 1,3:DNA

 # Link the first and third partitions
:smodel 1,3:TN93+>ASRV.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:

configAfterOption = 2;
