Hi Tina,

On Thu, 2014-06-05 at 00:42 -0400, Tina Lan wrote:
> Hi,
>   It would be really great if anyone could give me some advice on how to 
> activate the mauve assembly metrics within Mauve GUI. Thanks a lot!

What version of Mauve have you downloaded? The assembly metrics are only
available in the more recent snapshot versions, available here:
http://gel.ahabs.wisc.edu/mauve/snapshots

To use them, use progressiveMauve to align a pair of genomes with the
reference genome first, assembly second, then click the "balance scale"
icon that should appear in the top right corner.

Hope that helps,
-Aaron


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