View source for Mauve

[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Genomics]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|mauve}}
|{{#vardefine:url|http://gel.ahabs.wisc.edu/mauve/}}
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|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
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|{{#vardefine:faq|}}             <!--FAQ-->
|{{#vardefine:citation|}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
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<!--Description-->
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics.  Aligning whole genomes is a fundamentally different problem than aligning short sequences.

Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the amount of sequence being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours.
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==Environment Modules==
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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{{#if: {{#var: exe}}|==Additional Information==
See [http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/using-mauvealigner-from-the-command-line.html/ using mauve from the command-line] on how to use Mauve at the command line. You can also briefly run the main Gui by logging into the gui.rc.ufl.edu server. See [[GUI_Programs]] for details on connecting to the gui server.

;To run Mauve gui
: Run '<code>export _JAVA_OPTIONS="-Xmx<MEMORY>"</code>' where <MEMORY> is the maximum heap memory size to be used by Java for Mauve in Gigabytes (g) or Megabytes (m) before running '<code>Mauve</code>'. This will override the initial setting of 500m. Examples of memory values in mega- or gigabytes: "1500m" or "2g".
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{{#if: {{#var: pbs}}|==PBS Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
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<!--Policy-->
{{#if: {{#var: policy}}|==Usage Policy==
WRITE USAGE POLICY HERE (Licensing, usage, access).
|}}
<!--Performance-->
{{#if: {{#var: testing}}|==Performance==
WRITE_PERFORMANCE_TESTING_RESULTS_HERE
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<!--Faq-->
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:
WRITE_CITATION_HERE
|}}
<!--Installation-->
{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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