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THIS FILE IS OUT OF DATE
The current user guide resides online at http://gel.ahabs.wisc.edu/mauve/mauve-user-guide

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
Ctrl+p - print
print - Ctrl+p
'A problem of type 2094 has occured'. What the (heck) is that? What are the 2093 other problems I just missed to get to that one?

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.  Send reports to darling(at)cs.wisc.edu