'\" t
.\"     Title: gt-orffinder
.\"    Author: [FIXME: author] [see http://www.docbook.org/tdg5/en/html/author]
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 07/22/2020
.\"    Manual: GenomeTools Manual
.\"    Source: GenomeTools 1.6.1
.\"  Language: English
.\"
.TH "GT\-ORFFINDER" "1" "07/22/2020" "GenomeTools 1\&.6\&.1" "GenomeTools Manual"
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.SH "NAME"
gt-orffinder \- Identifies ORFs (open reading frames) in sequences\&.
.SH "SYNOPSIS"
.sp
\fBgt orffinder\fR [option \&...] [indexname] [GFF3_file \&...]
.SH "DESCRIPTION"
.PP
\fB\-types\fR
.RS 4
Specify regions which should be searched for open reading frames, e\&.g\&.
\fILTR_retrotransposon\fR
.RE
.PP
\fB\-allorfs\fR [\fIyes|no\fR]
.RS 4
search for all ORFs instead of only the longest (default: no)
.RE
.PP
\fB\-min\fR [\fIvalue\fR]
.RS 4
minimum length of ORF (default: 30)
.RE
.PP
\fB\-max\fR [\fIvalue\fR]
.RS 4
maximum length of ORF (default: 10000)
.RE
.PP
\fB\-v\fR [\fIyes|no\fR]
.RS 4
be verbose (default: no)
.RE
.PP
\fB\-o\fR [\fIfilename\fR]
.RS 4
redirect output to specified file (default: undefined)
.RE
.PP
\fB\-gzip\fR [\fIyes|no\fR]
.RS 4
write gzip compressed output file (default: no)
.RE
.PP
\fB\-bzip2\fR [\fIyes|no\fR]
.RS 4
write bzip2 compressed output file (default: no)
.RE
.PP
\fB\-force\fR [\fIyes|no\fR]
.RS 4
force writing to output file (default: no)
.RE
.PP
\fB\-seqfile\fR [\fIfilename\fR]
.RS 4
set the sequence file from which to take the sequences (default: undefined)
.RE
.PP
\fB\-encseq\fR [\fIfilename\fR]
.RS 4
set the encoded sequence indexname from which to take the sequences (default: undefined)
.RE
.PP
\fB\-seqfiles\fR
.RS 4
set the sequence files from which to extract the features use
\fI\-\-\fR
to terminate the list of sequence files
.RE
.PP
\fB\-matchdesc\fR [\fIyes|no\fR]
.RS 4
search the sequence descriptions from the input files for the desired sequence IDs (in GFF3), reporting the first match (default: no)
.RE
.PP
\fB\-matchdescstart\fR [\fIyes|no\fR]
.RS 4
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)
.RE
.PP
\fB\-usedesc\fR [\fIyes|no\fR]
.RS 4
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 (\fIIII\fR) and the first range position as offset (\fI1000001\fR) (default: no)
.RE
.PP
\fB\-regionmapping\fR [\fIstring\fR]
.RS 4
set file containing sequence\-region to sequence file mapping (default: undefined)
.RE
.PP
\fB\-help\fR
.RS 4
display help and exit
.RE
.PP
\fB\-version\fR
.RS 4
display version information and exit
.RE
.SH "REPORTING BUGS"
.sp
Report bugs to https://github\&.com/genometools/genometools/issues\&.