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

search for all ORFs instead of only the longest (default: no)

minimum length of ORF (default: 30)

maximum length of ORF (default: 10000)

be verbose (default: no)

redirect output to specified file (default: undefined)

write gzip compressed output file (default: no)

write bzip2 compressed output file (default: no)

force writing to output file (default: no)

set the sequence file from which to take the sequences (default: undefined)

set the encoded sequence indexname from which to take the sequences (default: undefined)

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

search the sequence descriptions from the input files for the desired sequence IDs (in GFF3), reporting the first match (default: 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)

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)

set file containing sequence-region to sequence file mapping (default: undefined)

display help and exit

display version information and exit