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