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I am trying to use the command: SEQUENCE_COMPARISON, but I don´t
understand the output, in the MATRIX_FILE.
I mean, I don´t know what each number means ( which one is the score
which I can use to compare different alignments)

For example, thix matrix is the result when  I use : RR_FILE =
'$(LIB)/gonnet.sim.mat' and my alignmet.

    sequenceA 514.40  297.72
    sequenceB 297.72  504.86

I suposse the score I have to compare is 297.72  (which changes in
different alignments).

My problem is that I am using another aligment server, with the same
parameters I use in Modeller , and it gives only the score 504.

Thanks in advance