The pairwise similarity of sequences in the current alignment is evaluated using a user specified residue-residue scores file.
The residue-residue scores, including gap-residue, and gap-gap scores, are read from file rr_file. The sequence pair score is equal to the average pairwise residue-residue score for all alignment positions that have at most max_gaps_match gaps (1 by default). If the gap-residue and gap-gap scores are not defined in matrix_file, they are set to the worst and best residue-residue score, respectively. If matrix_file is a similarity matrix, it is converted into a distance matrix ( ).
The comparison matrix is written in the PHYLIP format to file matrix_file.
The family variability as a function of alignment position is calculated as the RMS deviation of all residue - residue scores at a given position, but only for those pairs of residues that have at most max_gaps_match gaps (0, 1, or 2). The variability is written to file variability_file, as is the number of pairwise comparisons contributing to each positional variability. The variability, scaled by 0.1, is also written into the B field of the model mdl, which must correspond to the first sequence in the alignment.
Example: See alignment.id_table() command.