repeatoire - Online in the Cloud

PROGRAM:

NAME

repeatoire - part of mauveAligner package

DESCRIPTION

Allowed options:
--allow-redundant arg (=1)
allow redundant alignments?

--chain arg (=1)
chain seeds?

--extend arg (=1)
perform gapped extension on chains?

--window arg (=-1)
size of window to use during gapped extension

--gapopen arg (=0)
gap open penalty

--gapextend arg (=0)
gap extension penalty

--h arg (=0.00800000038)
Transition to Homologous

--help get help message

--highest arg (=procrast.highest) file containing highest scoring alignment
for each multiplicity

--l arg (=1)
minimum repeat length

--large-repeats arg (=0)
optimize for large repeats

--load-sml arg (=0)
try to load existing SML file?

--onlydirect arg (=0)
only process seed matches on same strand?

--onlyextended arg (=0)
only output extended matches?

--output arg
procrastAligner output

--percentid arg (=0)
min repeat family % id

--novel-subsets arg (=0)
find novel subset matches?

--novel-matches arg (=1)
use novel matches found during gapped extension?

--rmax arg (=500)
maximum repeat multiplicity (max copy number)

--rmin arg (=2)
minimum repeat multiplicity (min copy number)

--seeds arg
seed output file

--sequence arg
FastA sequence file

--small-repeats arg (=0)
optimize for small repeats

--score-out arg
output with corresponding score and alignment info

--solid arg (=0)
use solid/exact seeds?

--sp arg (=0)
minimum Sum-of-Pairs alignment score

--tandem arg (=1)
allow tandem repeats?

--two-hits arg (=0)
require two hits within w to trigger gapped extension?

--u arg (=0.00100000005)
Transition to Unrelated

--unalign arg (=1)
unalign non-homologous sequence?

--w arg (=0)
max gap width

--xmfa arg
XMFA format output

--xml arg
XML format output

--z arg (=0)
seed weight

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