alm_matrix : { ‘self’, ‘other’ }
Indicate for which MSA the sum-of-pairs score shall be calculated.
mat : None or numpy.array
If ‘other’ is chosen as an option for alm_matrix, define for
which matrix the sum-of-pairs score shall be calculated.
gap_weight : float (default=0)
The factor by which gaps in aligned columns contribute to the
calculation of the column score. When set to 0, gaps will be
ignored in the calculation. When set to 0.5, gaps will count half
as much as other characters.
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