bionic (1) mauveAligner.1.gz

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