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