[Jalview-discuss] Can I delete columns with no variation?

[James Procter]

Hello Sang Chul.

Sang Chul Choi wrote:
> I am wondering if I can delete columns  
> with no variation.
At this moment, you cannot - but I hope to introduce that functionality
in the next version.
 I also want to know if I could know the nucleotide
> percentage for each site.
Do you mean the proportion of each base at each site ?  Once again I
have to say no, for the moment. Jalview calculates the percentages
internally when it creates the consensus histogram, but it doesn't show
the full profile to the user. Again, I think this will be introduced in
the next release.

> Is there a function in Jalview to do the four gamete test?
Once again, no. Jalview's nucleotide analysis functions are very
primitive - if you can find another way to perform the test, then you
could create an annotation file to load back onto your sequences (or
alignments) so Jalview could view them. Have a look in the help
documentation to see details of the file formats.

I hope this helps
Jim.