'\" t
.\"     Title: gt-eval
.\"    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\-EVAL" "1" "02/28/2024" "GenomeTools 1\&.6\&.5" "GenomeTools Manual"
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.SH "NAME"
gt-eval \- Compare annotation files and show accuracy measures (prediction vs\&. reference)\&.
.SH "SYNOPSIS"
.sp
\fBgt eval\fR reference_file prediction_file
.SH "DESCRIPTION"
.PP
\fB\-nuc\fR [\fIyes|no\fR]
.RS 4
evaluate nucleotide level (memory consumption is proportional to the input file sizes) (default: yes)
.RE
.PP
\fB\-ltr\fR [\fIyes|no\fR]
.RS 4
evaluate a LTR retrotransposon prediction instead of a gene prediction (all LTR_retrotransposon elements are considered to have an undetermined strand) (default: no)
.RE
.PP
\fB\-ltrdelta\fR [\fIvalue\fR]
.RS 4
set allowed delta for LTR borders to be considered equal (default: 20)
.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\-help\fR
.RS 4
display help and exit
.RE
.PP
\fB\-version\fR
.RS 4
display version information and exit
.RE
.sp
The program shows sensitivity and specificity values for certain feature types (e\&.g\&., gene, mRNA, and exon)\&. For some feature types the number of missing and wrong features of that type is also shown\&. Thereby, \(lqmissing\(rq means the number of features of that type from the \(lqreference\(rq without overlap to a feature of that type from the \(lqprediction\(rq\&. Vice versa, \(lqwrong\(rq denotes the number of features of that type from the \(lqprediction\(rq without overlap to a feature of that type from the \(lqreference\(rq\&.
.SH "REPORTING BUGS"
.sp
Report bugs to https://github\&.com/genometools/genometools/issues\&.