prophecy creates a profile matrix file from a nucleic acid or a protein sequence alignment.

Here is a sample session with prophecy:

% prophecy
Creates matrices/profiles from multiple alignments
Input sequence set: globins.msf
Profile type
         F : Frequency
         G : Gribskov
         H : Henikoff
Select type [F]:
Enter a name for the profile [mymatrix]: globins
Enter threshold reporting percentage [75]:
Output file [globins.prophecy]:

Mandatory qualifiers (bold if not always prompted):

[-sequence] (seqset)

Sequence set USA.

-type (menu)

Select type.

-name (string)

Enter a name for the profile.

-threshold (integer)

Enter threshold reporting percentage.

-datafile (matrixf)

Scoring matrix.

-open (float)

Gap opening penalty.

-extension (float)

Gap extension penalty.

[-outf] (outfile)

Output filename.