Prophecy matrices

[Jack Leunissen]

Dear EMBOSS team,

Is it a known bug (or a feature) that PROPHECY ignores any scoring matrix you specify? Whatever you type, and in whatever way (prompt or flag), it insists on using the Epprofile matrix (which is reported wrongly as "pprofile").

I have been using versions 2.6.0 and 2.7.1, and both behave the same.

Regards,
Jack Leunissen
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