'\" t
.\"     Title: gt-seqmutate
.\"    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\-SEQMUTATE" "1" "07/22/2020" "GenomeTools 1\&.6\&.1" "GenomeTools Manual"
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.SH "NAME"
gt-seqmutate \- Mutate the sequences of the given sequence file(s)\&.
.SH "SYNOPSIS"
.sp
\fBgt seqmutate\fR [option \&...] [sequence_file \&...]
.SH "DESCRIPTION"
.PP
\fB\-rate\fR [\fIvalue\fR]
.RS 4
set the mutation rate (default: 1)
.RE
.PP
\fB\-width\fR [\fIvalue\fR]
.RS 4
set output width for FASTA sequence printing (0 disables formatting) (default: 0)
.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
For each position in the given sequences it is randomly determined with probability (mutation rate / 100) if the given position is mutated\&. If so, in 80% of the cases a substitution is performed, in 10% an insertion, and in 10% a deletion, respectively\&. For substitution and insertion events, the nucleotide is generated randomly without regard to the original nucleotide\&. That is, resubstitutions are possible\&. This procedure equals the one described on page 1867 of the following paper:
.sp
\fIT\&.D\&. Wu and C\&.K\&. Watanabe\&. GMAP: a genomic mapping and alignment program for mRNA and EST sequences\&. Bioinformatics, 21(9):1859\-1875, 2005\&.\fR
.SH "REPORTING BUGS"
.sp
Report bugs to https://github\&.com/genometools/genometools/issues\&.