genewise ($Name: wise2-2-0 $)
This program is freely distributed under a GPL. See -version for more info
Copyright (c) GRL limited: portions of the code are from separate copyrights

genewise <protein-file> <dna-file> in fasta format
 Options. In any order, '-' as filename (for any input) means stdin
 Dna      [-u,-v,-trev,-tabs,-fembl,-both]
 Protein  [-s,-t,-g,-e,-m]
 HMM      [-hmmer,-hname]
 Model    [-codon,-gene,-cfreq,-splice,-subs,-indel,-intron,-null]
 Alg      [-kbyte,-alg]
 Output   [-pretty,-genes,-genesf,-para,-sum,-cdna,-trans,-pep,-ace,-embl,-diana]
  ..cont  [-gff,-gener,-alb,-pal,-block,-divide]
 Standard [-help,-version,-silent,-quiet,-errorlog]

For more help go genewise -help.

See WWW help at http://www.sanger.ac.uk/Software/Wise2/