.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH REPEATOIRE "1" "April 2015" "repeatoire 1.2.0+4713" "User Commands"
.SH NAME
repeatoire \- part of mauveAligner package
.SH DESCRIPTION
.SS "Allowed options:"
.TP
\fB\-\-allow\-redundant\fR arg (=1)
allow redundant alignments?
.TP
\fB\-\-chain\fR arg (=1)
chain seeds?
.TP
\fB\-\-extend\fR arg (=1)
perform gapped extension on chains?
.TP
\fB\-\-window\fR arg (=\-1)
size of window to use during gapped
extension
.TP
\fB\-\-gapopen\fR arg (=0)
gap open penalty
.TP
\fB\-\-gapextend\fR arg (=0)
gap extension penalty
.TP
\fB\-\-h\fR arg (=0.00800000038)
Transition to Homologous
.TP
\fB\-\-help\fR
get help message
.TP
\fB\-\-highest\fR arg (=procrast.highest) file containing highest scoring alignment
for each multiplicity
.TP
\fB\-\-l\fR arg (=1)
minimum repeat length
.TP
\fB\-\-large\-repeats\fR arg (=0)
optimize for large repeats
.TP
\fB\-\-load\-sml\fR arg (=0)
try to load existing SML file?
.TP
\fB\-\-onlydirect\fR arg (=0)
only process seed matches on same strand?
.TP
\fB\-\-onlyextended\fR arg (=0)
only output extended matches?
.TP
\fB\-\-output\fR arg
procrastAligner output
.TP
\fB\-\-percentid\fR arg (=0)
min repeat family % id
.TP
\fB\-\-novel\-subsets\fR arg (=0)
find novel subset matches?
.TP
\fB\-\-novel\-matches\fR arg (=1)
use novel matches found during gapped
extension?
.TP
\fB\-\-rmax\fR arg (=500)
maximum repeat multiplicity (max copy
number)
.TP
\fB\-\-rmin\fR arg (=2)
minimum repeat multiplicity (min copy
number)
.TP
\fB\-\-seeds\fR arg
seed output file
.TP
\fB\-\-sequence\fR arg
FastA sequence file
.TP
\fB\-\-small\-repeats\fR arg (=0)
optimize for small repeats
.TP
\fB\-\-score\-out\fR arg
output with corresponding score and
alignment info
.TP
\fB\-\-solid\fR arg (=0)
use solid/exact seeds?
.TP
\fB\-\-sp\fR arg (=0)
minimum Sum\-of\-Pairs alignment score
.TP
\fB\-\-tandem\fR arg (=1)
allow tandem repeats?
.TP
\fB\-\-two\-hits\fR arg (=0)
require two hits within w to trigger gapped
extension?
.TP
\fB\-\-u\fR arg (=0.00100000005)
Transition to Unrelated
.TP
\fB\-\-unalign\fR arg (=1)
unalign non\-homologous sequence?
.TP
\fB\-\-w\fR arg (=0)
max gap width
.TP
\fB\-\-xmfa\fR arg
XMFA format output
.TP
\fB\-\-xml\fR arg
XML format output
.TP
\fB\-\-z\fR arg (=0)
seed weight