---
name: "mauveAligner"
section: "1"
platform: "linux"
package: "progressivemauve"
version: "1.2.0+4713+dfsg-5+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/mauveAligner"
---

# mauveAligner(1)

efficiently constructing multiple genome alignments

## 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