main ()

%(filename)s

Translates a fasta format file containing nucleotide sequences. Can filter translated sequences according to length, presence of unwanted characters (like X,*).

{{degap Gap characters (-.~) are removed as file is read.}} {{filter looks for a filterfile (-filter=filterfile) with instructions for rejection of sequences. Filterfile is of format: [character to find][max number of occurrences to allow]}} Example: if the filterfile looks like: 0 X 2 Sequences with > 0 's or > 2 X's will be rejected.

{{maxlen Reject translated sequences less than this length. Will apply to the length of the degapped sequence if -degap is selected. 100000}} {{minlen Set minimum length of translated sequence. 0}} {{f frame; specify reading frame 1, 2, or 3 1}} {{out Name of outfile.}} {{amb Ambiguity handling ambi codons containing IUPAC ambiguity characters will be translated if a unique amino acid is encoded. unambi causes any codon containing an ambiguity to be translated as an X.}} {{h Print documentation.}} {{v verbosity; 0 for no output. 1}} {{version print version info and exit}}

%(version)s