'\" t
.\"     Title: gt-tirvish
.\"    Author: [FIXME: author] [see http://www.docbook.org/tdg5/en/html/author]
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 02/28/2024
.\"    Manual: GenomeTools Manual
.\"    Source: GenomeTools 1.6.5
.\"  Language: English
.\"
.TH "GT\-TIRVISH" "1" "02/28/2024" "GenomeTools 1\&.6\&.5" "GenomeTools Manual"
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.el       .ds Aq '
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.SH "NAME"
gt-tirvish \- Identify Terminal Inverted Repeat (TIR) elements,such as DNA transposons\&.
.SH "SYNOPSIS"
.sp
\fBgt tirvish\fR [option \&...] \-index INDEXNAME
.SH "DESCRIPTION"
.PP
\fB\-index\fR [\fIstring\fR]
.RS 4
specify the name of the enhanced suffix array index (mandatory) (default: undefined)
.RE
.PP
\fB\-seed\fR [\fIvalue\fR]
.RS 4
specify minimum seed length for exact repeats (default: 20)
.RE
.PP
\fB\-mintirlen\fR [\fIvalue\fR]
.RS 4
specify minimum length for each TIR (default: 100)
.RE
.PP
\fB\-maxtirlen\fR [\fIvalue\fR]
.RS 4
specify maximum length for each TIR (default: 1000)
.RE
.PP
\fB\-mintirdist\fR [\fIvalue\fR]
.RS 4
specify minimum distance of TIRs (default: 500)
.RE
.PP
\fB\-maxtirdist\fR [\fIvalue\fR]
.RS 4
specify maximum distance of TIRs (default: 10000)
.RE
.PP
\fB\-mat\fR [\fIvalue\fR]
.RS 4
specify matchscore for extension\-alignment (default: 2)
.RE
.PP
\fB\-mis\fR [\fIvalue\fR]
.RS 4
specify mismatchscore for extension\-alignment (default: \-2)
.RE
.PP
\fB\-ins\fR [\fIvalue\fR]
.RS 4
specify insertionscore for extension\-alignment (default: \-3)
.RE
.PP
\fB\-del\fR [\fIvalue\fR]
.RS 4
specify deletionscore for extension\-alignment (default: \-3)
.RE
.PP
\fB\-xdrop\fR [\fIvalue\fR]
.RS 4
specify xdropbelowscore for extension\-alignment (default: 5)
.RE
.PP
\fB\-similar\fR [\fIvalue\fR]
.RS 4
specify TIR similarity threshold in therange [1\&.\&.100%] (default: 85\&.000000)
.RE
.PP
\fB\-overlaps\fR [\fI\&...\fR]
.RS 4
specify no|best|longest|all (default: best)
.RE
.PP
\fB\-mintsd\fR [\fIvalue\fR]
.RS 4
specify minimum length for each TSD (default: 2)
.RE
.PP
\fB\-maxtsd\fR [\fIvalue\fR]
.RS 4
specify maximum length for each TSD (default: 11)
.RE
.PP
\fB\-vic\fR [\fIvalue\fR]
.RS 4
specify the number of nucleotides (to the left and to the right) that will be searched for TSDs around 5\*(Aq and 3\*(Aq boundary of predicted TIRs (default: 60)
.RE
.PP
\fB\-hmms\fR
.RS 4
profile HMM models for domain detection (separate by spaces, finish with \-\-) in HMMER3 format Omit this option to disable pHMM search\&.
.RE
.PP
\fB\-pdomevalcutoff\fR [\fIvalue\fR]
.RS 4
global E\-value cutoff for pHMM search default 1E\-6
.RE
.PP
\fB\-pdomcutoff\fR [\fI\&...\fR]
.RS 4
model\-specific score cutoff choose from TC (trusted cutoff) | GA (gathering cutoff) | NONE (no cutoffs) (default: GA)
.RE
.PP
\fB\-maxgaplen\fR [\fIvalue\fR]
.RS 4
maximal allowed gap size between fragments (in amino acids) when chaining pHMM hits for a protein domain (default: 50)
.RE
.PP
\fB\-refseqs\fR [\fIstring\fR]
.RS 4
specify the name of the gene sequences to scan for inside candidates (default: undefined)
.RE
.PP
\fB\-seqids\fR [\fIyes|no\fR]
.RS 4
use sequence descriptions instead of sequence numbers in GFF3 output (default: yes)
.RE
.PP
\fB\-md5\fR [\fIyes|no\fR]
.RS 4
add MD5 hashes to seqids in GFF3 output (default: no)
.RE
.PP
\fB\-help\fR
.RS 4
display help for basic options and exit
.RE
.PP
\fB\-help+\fR
.RS 4
display help for all options 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\&.