'\" t
.\"     Title: gt-ltrharvest
.\"    Author: [FIXME: author] [see http://docbook.sf.net/el/author]
.\" Generator: DocBook XSL Stylesheets v1.79.1 <http://docbook.sf.net/>
.\"      Date: 07/29/2020
.\"    Manual: GenomeTools Manual
.\"    Source: GenomeTools 1.6.1
.\"  Language: English
.\"
.TH "GT\-LTRHARVEST" "1" "07/29/2020" "GenomeTools 1\&.6\&.1" "GenomeTools Manual"
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.SH "NAME"
gt-ltrharvest \- Predict LTR retrotransposons\&.
.SH "SYNOPSIS"
.sp
\fBgt ltrharvest\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\-range\fR [\fIstart\fR \fIend\fR]
.RS 4
specify range in the input sequence(s) in which LTR pairs are searched (default: [0\&.\&.0])
.RE
.PP
\fB\-seed\fR [\fIvalue\fR]
.RS 4
specify minimum seed length for exact repeats (default: 30)
.RE
.PP
\fB\-minlenltr\fR [\fIvalue\fR]
.RS 4
specify minimum length for each LTR (default: 100)
.RE
.PP
\fB\-maxlenltr\fR [\fIvalue\fR]
.RS 4
specify maximum length for each LTR (default: 1000)
.RE
.PP
\fB\-mindistltr\fR [\fIvalue\fR]
.RS 4
specify minimum distance of LTR startpositions (default: 1000)
.RE
.PP
\fB\-maxdistltr\fR [\fIvalue\fR]
.RS 4
specify maximum distance of LTR startpositions (default: 15000)
.RE
.PP
\fB\-similar\fR [\fIvalue\fR]
.RS 4
specify similaritythreshold in range [1\&.\&.100%] (default: 85\&.000000)
.RE
.PP
\fB\-mintsd\fR [\fIvalue\fR]
.RS 4
specify minimum length for each TSD (default: 4)
.RE
.PP
\fB\-maxtsd\fR [\fIvalue\fR]
.RS 4
specify maximum length for each TSD (default: 20)
.RE
.PP
\fB\-motif\fR [\fIstring\fR]
.RS 4
specify 2 nucleotides startmotif + 2 nucleotides endmotif:
\fB*\fR* (default: undefined)
.RE
.PP
\fB\-motifmis\fR [\fIvalue\fR]
.RS 4
specify maximum number of mismatches in motif [0,3] (default: 4)
.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 and/or motifs around 5\*(Aq and 3\*(Aq boundary of predicted LTR retrotransposons (default: 60)
.RE
.PP
\fB\-overlaps\fR [\fI\&...\fR]
.RS 4
specify no|best|all (default: best)
.RE
.PP
\fB\-xdrop\fR [\fIvalue\fR]
.RS 4
specify xdropbelowscore for extension\-alignment (default: 5)
.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\-v\fR [\fIyes|no\fR]
.RS 4
verbose mode (default: no)
.RE
.PP
\fB\-tabout\fR [\fIyes|no\fR]
.RS 4
show
\fIold\fR
tabular output instead of GFF3 on stdout (default: yes)
.RE
.PP
\fB\-seqids\fR [\fIyes|no\fR]
.RS 4
use sequence descriptions instead of sequence numbers in GFF3 output (default: no)
.RE
.PP
\fB\-md5\fR [\fIyes|no\fR]
.RS 4
add MD5 hashes to seqids in GFF3 output (default: no)
.RE
.PP
\fB\-longoutput\fR [\fIyes|no\fR]
.RS 4
additional motif/TSD output (default: no)
.RE
.PP
\fB\-out\fR [\fIstring\fR]
.RS 4
specify FASTA outputfilename (default: undefined)
.RE
.PP
\fB\-outinner\fR [\fIstring\fR]
.RS 4
specify FASTA outputfilename for inner regions (default: undefined)
.RE
.PP
\fB\-gff3\fR [\fIstring\fR]
.RS 4
specify GFF3 outputfilename (default: undefined)
.RE
.PP
\fB\-offset\fR [\fIvalue\fR]
.RS 4
offset added to GFF3 coordinates (default: 0)
.RE
.PP
\fB\-scan\fR [\fIyes|no\fR]
.RS 4
scan the index sequentially instead of mapping it into memory entirely (default: yes)
.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 "ADDITIONAL INFORMATION"
.sp
For detailed information, please refer to the manual of ltrharvest\&.
.SH "REPORTING BUGS"
.sp
Report bugs to https://github\&.com/genometools/genometools/issues\&.