jordibc / mauve

A genome alignment and visualization system

This repository contains a simple update of the original Mauve code to run with a modern Java version.

To use Mauve, first download this repository, change to its directory, and compile with:

ant compile  # compiles all the java files into class files
ant jar  # creates Mauve.jar

and then you can run Mauve with:

java -jar Mauve.jar

You may want to use a different maximum heap size with the appropriate -Xmx option, for example java -Xmx10G -jar Mauve.jar for a 10 GB memory size. Depending on what you do, Mauve may need different values to operate correctly.

There is more information about the (no longer maintained) Mauve, including a user guide, at https://darlinglab.org/mauve/mauve.html

The documentation below is copied from the original repository and may be out of date.

Mauve Overview

Mauve is a program for performing comaparative analyses of genomes. To generate a new genome alignment with Mauve, select 'Align' from the File menu. To open an existing genome alignment, select 'Open' from the file menu.

Aligment Overview

Once Align has been selected from the File menu, a new window pops up that allows alignment parameters to be specified. The first thing to do is add sequences to align using the Add Sequence button. Sequence files can be in FastA (.fas), Genbank (.gbk), or DNAStar (.seq) formats and MUST have the corresponding filename extension. (Otherwise mauveAligner will crash.)

The output file selection is optional. If an output file is not specified, Mauve will save the alignment in your temp directory.

The Minimum LCB weight parameter specifies the minimum number of matching base pairs Mauve should use to determine wether a rearranged segment of the chromosome is significant. Rearrangements below the weight threshold are treated as random matches and are discarded.

The Minimum Island size parameter specifies the number of consecutive gaps in the alignment between a pair of sequences that mauveAligner should consider to be an island in one of the sequences. The location of islands is written to <output filename>.islands.

The Full Alignment option allows Mauve to perform a recursive alignment of gapped regions, allowing for complete coverage over the genomes. In general you will want to use this option.

If Minimum LCB weight, Minimum Island size, and Full Alignment are not specified, Mauve defaults to simply locating matches between the sequences without trying to determine boundaries of rearrangement. This can be useful because Mauve will not filter out subset matches in this execution mode, allowing a better perspective of subset homology (try using the Y color scheme with this).

If Mauve is performing an alignment, it outputs the phylogenetic guide tree to <output filename>.guide_tree and outputs a gapped alignment to <output filename>.alignment.

Basic keyboard interface commands

• up arrow - Zoom in

• down arrow - Zoom out

• Ctrl + left arrow - Shift left

• Ctrl + right arrow - Shift right

• Ctrl + Shift + left arrow - Big shift left

• Ctrl + Shift + right arrow - Big shift right

• o - Generalized offset color scheme

• i - Normalized generalized offset color scheme

• u - Multiplicity type color scheme

• y - Normalized multiplicity type color scheme

• p - Multiplicity color scheme

• l - LCB color scheme

• Shift + L - Toggle LCB homology tracking lines

• Shift + S - Lock scales to the longest range of sequence currently in view

• Ctrl + P - Print

Mouse interface

Click on a matching region to highlight the corresponding matches in other sequences right-click on a matching region for a pop-up menu to center the display on that match.

Running Mauve in Linux

A shell script called "Mauve" has been included that calls java with the appropriate parameters to execute Mauve. From the mauve directory you should be able to run Mauve by entering the command:

./Mauve

You may need to adjust the java command line used by the script to execute Mauve.

Bugs

Yes there are bugs. Do not send reports anymore to aaron.darling(at)uts.edu.au since the software is no longer maintained. But if you open an issue in this repository, we may figure out a solution together.