Can I delete columns with no variation?

Hi,

I have a couple of questions. I am wondering if I can delete columns with no variation. I also want to know if I could know the nucleotide percentage for each site.

Is there a function in Jalview to do the four gamete test?

Thank you,

Sang Chul

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.