NAME

       gt-orffinder - Identifies ORFs (open reading frames) in sequences.

SYNOPSIS

       gt orffinder [option ...] [indexname] [GFF3_file ...]

DESCRIPTION

       -types
           Specify regions which should be searched for open reading frames, e.g.
           LTR_retrotransposon

       -allorfs [yes|no]
           search for all ORFs instead of only the longest (default: no)

       -min [value]
           minimum length of ORF (default: 30)

       -max [value]
           maximum length of ORF (default: 10000)

       -v [yes|no]
           be verbose (default: no)

       -o [filename]
           redirect output to specified file (default: undefined)

       -gzip [yes|no]
           write gzip compressed output file (default: no)

       -bzip2 [yes|no]
           write bzip2 compressed output file (default: no)

       -force [yes|no]
           force writing to output file (default: no)

       -seqfile [filename]
           set the sequence file from which to take the sequences (default: undefined)

       -encseq [filename]
           set the encoded sequence indexname from which to take the sequences (default:
           undefined)

       -seqfiles
           set the sequence files from which to extract the features use -- to terminate the list
           of sequence files

       -matchdesc [yes|no]
           search the sequence descriptions from the input files for the desired sequence IDs (in
           GFF3), reporting the first match (default: no)

       -matchdescstart [yes|no]
           exactly match the sequence descriptions from the input files for the desired sequence
           IDs (in GFF3) from the beginning to the first whitespace (default: no)

       -usedesc [yes|no]
           use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence
           entries. If a description contains a sequence range (e.g., III:1000001..2000000), the
           first part is used as sequence ID (III) and the first range position as offset
           (1000001) (default: no)

       -regionmapping [string]
           set file containing sequence-region to sequence file mapping (default: undefined)

       -help
           display help and exit

       -version
           display version information and exit

REPORTING BUGS

       Report bugs to <gt-users@genometools.org>.