Automated GLOCSA scores?

[Bruce Kirchoff]

Although the GLOCSA scores are a huge improvement over having no way
to judge the suitability of the alignment, we do not know if the
default parameters give us the best measure of overall alignment. We
have discussed this in the context of allowing the user to vary these
parameters through an advanced options menu, but I have another idea.

Would it be possible to have the program very the parameters in some
kind of systematic way, calculate GLOCSA scores for each
parameterization, and create a graph that shows how the score varies
with parameter. The shape of the graph could be used as an indication
of the goodness of the alignment. In making this suggestion I am
assuming that the alignment is not changing during the calculation
process. So we have one alignment, and a graph of a number of
different ways of measuring the quality of that alignment. Since there
are three parameters to vary, it would have to be a three-dimensional
graph. I don't know if this would cause computational problems, or
display problems.

I would be interested in knowing what other people thought of this
idea, especially Helga.

Bruce