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