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