Man page - mauvealigner(1)
Packages contains this manual
apt-get install progressivemauve
Manual
MAUVEALIGNER
NAMESYNOPSIS
DESCRIPTION
OPTIONS
Gapped alignment controls:
Signed permutation matrix options:
Alignment output options:
NAME
mauveAligner - efficiently constructing multiple genome alignments
SYNOPSIS
mauveAligner [options] <seq1 filename> <sml1 filename> ... <seqN filename> <smlN filename>
DESCRIPTION
The mauveAligner and progressiveMauve alignment algorithms have been implemented as command-line programs included with the downloadable Mauve software. When run from the command-line, these programs provide options not yet available in the graphical interface.
OPTIONS
--output= <file> Output file name.
Prints to screen by default
--mums
Find MUMs only, do
not attempt to determine locally collinear
blocks (LCBs)
--no-recursion
Don’t perform recursive anchor
identification (implies
--no-gapped-alignment
)
--no-lcb-extension
If determining LCBs, don’t
attempt to extend the
LCBs
--seed-size=
<number> Initial seed match size,
default is log_2( average
seq. length )
--max-extension-iterations=
<number> Limit LCB
extensions to this number
of attempts, default is 4
--eliminate-inclusions
Eliminate linked inclusions in
subset matches.
--weight=
<number> Minimum LCB weight in base pairs
per sequence
--match-input=
<file> Use specified match file
instead of searching for
matches
--lcb-match-input
Indicates that the match input file
contains matches
that have been clustered into LCBs
--lcb-input=
<file> Use specified lcb file instead
of constructing LCBs
(skips LCB generation)
--scratch-path=
<path> For large genomes, use a
directory for storage
of temporary data. Should be given two or more times to with
different
paths.
--id-matrix=
<file> Generate LCB stats and write
them to the specified
file
--island-size=
<number> Find islands larger than
the given number
--island-output=
<file> Output islands the given
file (requires
--island-size
)
--backbone-size=
<number> Find stretches of
backbone longer than the
given number of b.p.
--max-backbone-gap=
<number> Allow backbone to be
interrupted by gaps up
to this length in b.p.
--backbone-output=
<file> Output islands the given
file (requires
--island-size
)
--coverage-output=
<file> Output a coverage list to
the specified file
(- for stdout)
--repeats
Generates a repeat map. Only one sequence can
be specified
--output-guide-tree=
<file> Write out a guide tree
to the designated
file
--collinear
Assume that input sequences are
collinear--they have no
rearrangements
Gapped alignment controls:
--no-gapped-alignment
Don’t perform a gapped alignment
--max-gapped-aligner-length=
<number> Maximum
number of base pairs to
attempt aligning with the gapped aligner
--min-recursive-gap-length=
<number> Minimum size
of gaps that Mauve
will perform recursive MUM anchoring on (Default is 200)
Signed permutation matrix options:
--permutation-matrix-output=
<file>
Write out the LCBs as a signed
permutation matrix to the given file
--permutation-matrix-min-weight=
<number> A
permutation matrix will be
written for every set of LCBs with weight between this value
and the
value of
--weight
Alignment output options:
--alignment-output-dir=
<directory>
Outputs a set of alignment files
(one per LCB) to a given directory
--alignment-output-format=
<directory> Selects the
output format for
--alignment-output-dir
--output-alignment=
<file> Write out an XMFA format
alignment to the
designated file
Supported alignment output formats are: phylip, clustal, msf, nexus, mega, codon