Pred2ary has the following syntax:
java pred2ary [-?] [--] [-help] [-file] networks -p prediction_protein_file [-op prediction_output_file] [-o output_file] [-combine] [-choose N] [-blastlocal] [-blast] [-blastnet URL] [-psiblastlocal] [-psiblast] [-psiblastnet URL] Run with no options to get the interactive version. -?, --, or -help - describes all the options -pr - prediction set (readable protein or profile format) (here's a description of possible formats.) -op - prediction set output file (EA format, by default) YAPF, PDB, CASP3 format can be specified by file suffix (i.e. x.yapf) -o - output file [stdout] -file - means the jury of networks is in a file in your computer. (rather than one included in the package) -combine - combine all proteins in input file into 1 profile. (for loading a profile stored in a bunch of FASTA files) -choose N - choose the n'th sequence in each profile, starting at 0. (same effect as clicking on the n'th sequence) -blastlocal - run BLAST (locally, using 'blastall') on each protein. -blast - run BLAST (over net, at NCBI) on each protein. -blastnet URL - run BLAST (over net, at some URL) on each protein. -psiblastlocal - run PSI-BLAST (locally, using 'blastpgp') on each protein. -psiblast - run PSI-BLAST (over net, at NCBI) on each protein. -psiblastnet URL - run PSI-BLAST (over net, at some URL) on each protein. networks can be 'small', 'medium', or 'large', or in a user-specified file, if you use the -file option. (here's a description of the included juries)