---
name: "repeatoire"
section: "1"
platform: "linux"
package: "progressivemauve"
version: "1.2.0+4713+dfsg-5+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/repeatoire"
---

# repeatoire(1)

part of mauveAligner package

## 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