Hiding columns with many gaps

Hi all,

Sorry to bring this up from 2011



><i> Hi everyone,
</i>> ><i> Sorry if this is something that has been discussed before, I looked
</i>><i> for it and couldn't find any info.
</i>> ><i> In large multiple alignments, it can be convenient to hide positions
</i>><i> (columns) where more than a certain fraction of sequences have gaps.
</i>><i> I've seen that option in other editors (e.g. MUST). Is there a way to
</i>><i> do this in Jalview? If not, does anyone think it would be worthwhile
</i>> *to implement?*

I am having the same problem now and I can’t figure out how to do this.

Has anything been done in this direction?

Right now I am using a simple script (awk/sed) to remove columns of gaps from the alignment and loading multiple files into jalview (ie: original file + gaps over 90% deleted + gaps over 75% deleted). Does anybody have a better solution?

Thanks very much in advance


Hi Rafael.

We’re actually working on a new dialog for doing exactly this kind of operation. It currently works on the alignment annotation rows, but could easily be extended to work on other (non-visible) column wise properties such as gap percentage.

Try the jalview development version and look under the ‘Select’ menu to try out the new dialog. Any comments/requests can be added over at



On 13/01/2015 13:09, Rafael Fernández Leiro wrote:

Hi Rafa,

I have installed the development version to try this out, but I can’t see the “select by annotation” menu. I am running the mac version.

Try this build:

The new dialog is opened from the menu option at the bottom of the 'Select' drop down menu.

Currently, Jalview doesn't show the number/proportion of gaps as an annotation row that can be used to mark selections... we'll have a think to see how we can do it !



On 13/01/2015 13:53, Rafael Fernández Leiro wrote: