[Jalview-discuss] annotation for nucleotide alignments

[Stephanie Blandin]

Hi there,

I'm trying to color a nucleotide alignment by annotation (conservation in this case), so that only the non conserved nucleotides are highlighted in color. See attached document below for an idea of what I need. I managed to do it previously (I was working with a previous version of Jalview - v9 I believe for macs - but I am not sure the issue comes from that).
Now, I'm trying to do the same with another alignment and with Jalview v10, but it is not possible to select the option "by conservation" (and the accompanying "Modify Conservation Threshold..."), and when I select the option "by annotation", the window that pops up is empty. Coherently, when I select "Show annotations", it says that the alignment has no annotations.
So how can I transfer the conservation plot that is visible in ClustalX for instance (grey bar with dents when nucleotides are not conserved) to annotate my alignment in jalview? Or should I save the alignment under a different format than the clustal format (.aln) to have this conservation included in the file? Note: I usually use muscle to align sequences.
Sorry for this very basic question, and thanks in advance for your help!
Best,

Steph.


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