repeatoire(1) part of mauveAligner package


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
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