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MAUVEALIGNER(1) - Linux man page online | User commands

Efficiently constructing multiple genome alignments.

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April 2015
MAUVEALIGNER(1) User Commands MAUVEALIGNER(1)

NAME

mauveAligner - efficiently constructing multiple genome alignments

SYNOPSIS

mauveAligner [options] <seq1 filename> <sml1 filename> ... <seqN filename> <smlN file‐ name>

DESCRIPTION

The mauveAligner and progressiveMauve alignment algorithms have been implemented as com‐ mand-line programs included with the downloadable Mauve software. When run from the com‐ mand-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-align‐ ment) --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 genera‐ tion) --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
mauveAligner 1.2.0+4713 April 2015 MAUVEALIGNER(1)
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mauveAligner(1) referred by addUnalignedIntervals(1)
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