[ssml] HMM

[Kevin Karplus]

One can write a simple HMM scoring program in a few lines, but it will
be rather slow.  Training takes more lines.  Doing sequence weighting
take still more.  Doing space-efficient scoring with recovery of
alignment takes quite a few.  Handling various different null models
takes more lines.  Handling calibration of the E-values takes some
more lines.

After a while, it all adds up.