Hi Uwe, this information might only be implicit in the documentation.
Despite its use of MUSCLE, progressiveMauve only computes DNA-level
genome alignments. I am not aware of any software to compute protein-
level genome alignments (though it's been a while since I looked
around), possibly because the concept of a positional homology genome
alignment becomes less useful at the high levels of evolutionary
divergence that would require a switch to amino acid alignment. For
pairwise genome alignment there is a protein mode in MUMmer. For
multiple genomes you might look at gene family clustering approaches.
-Aaron
On Wed, 2017-03-08 at 13:00 +0100, Uwe Menzel wrote:
> Dear list,
>
> as a newbie: how do I find out if progressiveMauve works on DNA or
> AA?
> The format specification provided is for DNA.
> On the other hand, Mauve uses Clustal and muscle alignment tools ...
>
> Thanks!
>
>
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--
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia
http://darlinglab.org
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