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