repeatoire(1)

repeatoire1

Part of mauvealigner package

Overview

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

Releases

Unchanged in 5 releases since Debian 9 (Stretch).

  1. 9–13

From progressivemauve 1.2.0+4713+dfsg-5+b3 in Debian 13 (Trixie). Parsed by carta from the page's man source.