Hi Aleksander,
No the guide tree is not used in the SNP extraction. Did your
progressiveMauve run generate the .backbone and .bbcols files?
Are you generating the SNP file from the command line or within the
viewer? Are there any messages in either the terminal or the console
log window?
Best,
-Aaron
On Tue, 2016-12-13 at 15:07 +0100, Aleksander Mahnič wrote:
> Hi all,
>
> I have some problems with SNP extraction from alignment of 48 genomes
> (the output file remains empty).
> I noticed, that we did not set the progressiveMauve to save the guide
> tree. Could this play a role in SNP extract failing?
>
> If so.. Is there a fast option to make a guide tree from the
> alignment or is it easier to just run alignment again?
>
> Thank you.
>
> Best,
> Aleksander
>
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