> Where can I see which version are being used?

You can see both the Galaxy tool version and the Cuffdiff tool version (when 
available) by clicking on the 'view details' icon (the 'i' at the bottom of an 
expanded dataset). Right now the Cuffdiff version is not displayed, but that 
will change when our server is updated.

> What does Cuffdiff(version 0.0.5) mean then?

That is the version of the Galaxy wrapper; the wrapper provides the interface 
between Cuffdiff and Galaxy.

> What version was it before?

I think Cuffdiff version was 1.3.1 previously.
> I look forward to the update, will that mean another version of Cuffdiff 
> again?

The wrapper will be updated but not Cuffdiff itself.


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