gp_mkmtx is supposed to be a tool for an easy creation of matrices for the gp_matrix program. It takes a set of sequences, calculates the frequency of a nucleotide at each position starting from the first nucleotide and ending with the last nucleotide of the shortest sequence. For each position, four values are printed in a row, respectively for A, C, G and T/U. Each value is the logarithm of the calculated frequency (logarythmisation can be suppresed with the -l option). If the -g option is used, prior to the logarithmic scaling the values are diveded by the expected frequency at the given GC contents (that is, for example, at GC=50%, 0.25 for each nucleotide).
gp_mkmtx -g 50 somesequence.fasta somesequence.mtx
will produce a matrix file somesequence.mtx which, after some editing, will be directly suitable for the gp_matrix program.
All Genpak programs complain in situations you would also complain, like when they cannot find a sequence you gave them or the sequence is not valid.
The Genpak programs do not write over existing files. I have found this feature very useful :-)
I'm sure there are plenty left, so please mail me if you find them. I tried to clean up every bug I could find.
January Weiner III <email@example.com>