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.\"     Title: gthconsensus
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.20
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "GTHCONSENSUS" "1" "" "\ \&" "\ \&"
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.SH "NAME"
gthconsensus \- build consensus spliced alignments
.SH "SYNOPSIS"
.sp
\fBgthconsensus\fP [option ...] [file ...]
.SH "DESCRIPTION"
.sp
Show GenomeThreader output files containing intermediate results and assemble
the contained spliced alignments to consensus spliced alignments.
.SH "OPTIONS"
.sp
\fB\-translationtable\fP
.RS 4
set the codon translation table used for codon translation in
matching, DP, and output
default: 1
.RE
.sp
\fB\-v\fP
.RS 4
be verbose
default: no
.RE
.sp
\fB\-xmlout\fP
.RS 4
show output in XML format
default: no
.RE
.sp
\fB\-gff3out\fP
.RS 4
show output in GFF3 format
default: no
.RE
.sp
\fB\-md5ids\fP
.RS 4
show MD5 fingerprints as sequence IDs
default: no
.RE
.sp
\fB\-o\fP
.RS 4
redirect output to specified file
default: undefined
.RE
.sp
\fB\-gzip\fP
.RS 4
write gzip compressed output file
default: no
.RE
.sp
\fB\-bzip2\fP
.RS 4
write bzip2 compressed output file
default: no
.RE
.sp
\fB\-force\fP
.RS 4
force writing to output file
default: no
.RE
.sp
\fB\-gs2out\fP
.RS 4
output in old GeneSeqer2 format
default: no
.RE
.sp
\fB\-minalignmentscore\fP
.RS 4
set the minimum alignment score for spliced alignments to be
included into the set of spliced alignments
default: 0.00
.RE
.sp
\fB\-maxalignmentscore\fP
.RS 4
set the maximum alignment score for spliced alignments to be
included into the set of spliced alignments
default: 1.00
.RE
.sp
\fB\-mincoverage\fP
.RS 4
set the minimum coverage for spliced alignments to be
included into the set of spliced alignments
default: 0.00
.RE
.sp
\fB\-maxcoverage\fP
.RS 4
set the maximum coverage for spliced alignments to be
included into the set of spliced alignments
default: 9999.99
.RE
.sp
\fB\-intermediate\fP
.RS 4
stop after calculation of spliced alignments and output
results in reusable XML format. Do not process this output
yourself, use the ``normal\*(Aq\*(Aq XML output instead!
default: no
.RE
.sp
\fB\-help\fP
.RS 4
display help for basic options and exit
.RE
.sp
\fB\-help+\fP
.RS 4
display help for all options and exit
.RE
.sp
\fB\-version\fP
.RS 4
display version information and exit
.RE