'\" t
.\"     Title: gt-genomediff
.\"    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\-GENOMEDIFF" "1" "02/28/2024" "GenomeTools 1\&.6\&.5" "GenomeTools Manual"
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.SH "NAME"
gt-genomediff \- Calculates Kr: pairwise distances between genomes\&.
.SH "SYNOPSIS"
.sp
\fBgt genomediff\fR [option \&...] (INDEX | \-indexname NAME SEQFILE SEQFILE [\&...])
.SH "DESCRIPTION"
.PP
\fB\-indextype\fR [\fI\&...\fR]
.RS 4
specify type of index, one of: esa|pck|encseq\&. Where encseq is an encoded sequence and an enhanced suffix array will be constructed only in memory\&. (default: encseq)
.RE
.PP
\fB\-indexname\fR [\fIstring\fR]
.RS 4
Basename of encseq to construct\&. (default: undefined)
.RE
.PP
\fB\-unitfile\fR [\fIfilename\fR]
.RS 4
specifies genomic units, see below for description\&. (default: undefined)
.RE
.PP
\fB\-mirrored\fR [\fIyes|no\fR]
.RS 4
virtually append the reverse complement of each sequence (default: no)
.RE
.PP
\fB\-pl\fR [\fIvalue\fR]
.RS 4
specify prefix length for bucket sort recommendation: use without argument; then a reasonable prefix length is automatically determined\&. (default: 0)
.RE
.PP
\fB\-dc\fR [\fIvalue\fR]
.RS 4
specify difference cover value (default: 0)
.RE
.PP
\fB\-memlimit\fR [\fIstring\fR]
.RS 4
specify maximal amount of memory to be used during index construction (in bytes, the keywords
\fIMB\fR
and
\fIGB\fR
are allowed) (default: undefined)
.RE
.PP
\fB\-scan\fR [\fIyes|no\fR]
.RS 4
do not load esa index but scan it sequentially\&. (default: yes)
.RE
.PP
\fB\-thr\fR [\fIvalue\fR]
.RS 4
Threshold for difference (du, dl) in divergence calculation\&. default: 1e\-9
.RE
.PP
\fB\-abs_err\fR [\fIvalue\fR]
.RS 4
absolute error for expected shulen calculation\&. default: 1e\-5
.RE
.PP
\fB\-rel_err\fR [\fIvalue\fR]
.RS 4
relative error for expected shulen calculation\&. default: 1e\-3
.RE
.PP
\fB\-M\fR [\fIvalue\fR]
.RS 4
threshold for minimum logarithm\&. default: DBL_MIN
.RE
.PP
\fB\-v\fR [\fIyes|no\fR]
.RS 4
be verbose (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
.sp
The genomediff tool only accepts DNA input\&.
.sp
When used with sequence files or encseq, an enhanced suffix array will be built in memory\&. The ESA will not be created completely, but construction will use \fI\-memlimit\fR as a threshold and build it partwise, calculating the Shu\-length for each part\&.
.sp
File format for option \fI\-unitfile\fR (in Lua syntax):
.sp
.if n \{\
.RS 4
.\}
.nf
units = {
 genome1 = { "path/file1\&.fa", "file2\&.fa" },
 genome2 = { "file3\&.fa", "path/file4\&.fa" }
}
.fi
.if n \{\
.RE
.\}
.sp
Give the path to the files as they were given to the encseq tool! You can use
.sp
.if n \{\
.RS 4
.\}
.nf
$ gt encseq info INDEXNAME
.fi
.if n \{\
.RE
.\}
.sp
to get a list of files in an encoded sequence\&.
.sp
Comment lines in Lua start with \fI\-\-\fR and will be ignored\&.
.sp
See GTDIR/testdata/genomediff/unitfile1\&.lua for an example\&.
.sp
Options \fI\-pl\fR, \fI\-dc\fR and \fI\-memlimit\fR are options to influence ESA construction\&.
.SH "REPORTING BUGS"
.sp
Report bugs to <willrodt@zbh\&.uni\-hamburg\&.de>\&.