Man page - gt-orffinder(1)
Packages contains this manual
- gt-readjoiner(1)
- gt-cds(1)
- gt-extractfeat(1)
- gt-dupfeat(1)
- gt-select(1)
- gt-encseq(1)
- gt-matstat(1)
- gt-md5_to_id(1)
- gt-seqmutate(1)
- gt-seqtranslate(1)
- gt-mkfeatureindex(1)
- gt-dot(1)
- gt-compreads-decompress(1)
- gt-compreads-refcompress(1)
- gt-condenseq(1)
- gt-readjoiner-prefilter(1)
- gt-seqstat(1)
- gt-readjoiner-overlap(1)
- gt-splicesiteinfo(1)
- gt-prebwt(1)
- gt-extractseq(1)
- gt-encseq2spm(1)
- gt-convertseq(1)
- gt-clean(1)
- gt-encseq-encode(1)
- gt-ltrclustering(1)
- gt-seq(1)
- gt-ltrharvest(1)
- gt-sequniq(1)
- gt-inlineseq_split(1)
- gt-mergefeat(1)
- gt-splitfasta(1)
- gt-gtf_to_gff3(1)
- gt-ltrdigest(1)
- gt-seqfilter(1)
- gt-featureindex(1)
- gt-inlineseq_add(1)
- gt-speck(1)
- gt-mmapandread(1)
- gt-tallymer-mkindex(1)
- gt-seed_extend(1)
- gt-hop(1)
- gt-sketch(1)
- gt-repfind(1)
- gt-shulengthdist(1)
- gt-sketch_page(1)
- gt-gff3(1)
- gt-stat(1)
- gt-gff3validator(1)
- gt-packedindex(1)
- gt-merge(1)
- gt-wtree(1)
- gt-encseq-bitextract(1)
- gt-seqids(1)
- gt-readjoiner-assembly(1)
- gt-tirvish(1)
- gt-uniquesub(1)
- gt-encseq-sample(1)
- gt-chseqids(1)
- gt-compreads-compress(1)
- gt-scriptfilter(1)
- gt-seqtransform(1)
- gt-eval(1)
- gt-genomediff(1)
- gt-congruence(1)
- gt-chain2dim(1)
- gt-tallymer(1)
- gt-tagerator(1)
- gt-loccheck(1)
- gt-encseq-info(1)
- gt-snpper(1)
- gt-bed_to_gff3(1)
- gt(1)
- gt-matchtool(1)
- gt-simreads(1)
- gt-csa(1)
- gt-tallymer-occratio(1)
- gt-encseq-check(1)
- gt-tallymer-search(1)
- gt-encseq-bench(1)
- gt-shredder(1)
- gt-gff3_to_gtf(1)
- gt-orffinder(1)
- gt-encseq-decode(1)
- gt-compreads(1)
- gt-encseq-md5(1)
- gt-uniq(1)
- gt-congruence-spacedseed(1)
- gt-id_to_md5(1)
- gt-seqorder(1)
- gt-compreads-refdecompress(1)
- gt-fingerprint(1)
- gt-fastq_sample(1)
- gt-interfeat(1)
apt-get install genometools
Manual
GT-ORFFINDER
NAMESYNOPSIS
DESCRIPTION
REPORTING BUGS
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 https://github.com/genometools/genometools/issues.