Removing constant sites from alignment

Korbinian Strimmer strimmer at ermine.ox.ac.uk
Wed Jul 12 15:49:59 EST 2000

On Wed, 12 Jul 2000, Nicolas Le Novere wrote:

> I'd like to remove all constant sites from
> DNA alignment and print out this > reduced data set for visual
> inspection. Is there a program to do this > automatically or do I have
> to remove them by hand with a alignment editor?
> I extend the question: Is there a routine to remove non-informative
> sites, i.e. constant sites, or sites which do not containt at least
> two states present twice?

Yes, there is.  The class pal.alignment.StrippedAlignment in PAL
(http://www.pal-project.org) has methods to do just this.

If you prefer more comfort (rather than programming Java yourself) you can
alternatively use the program REWRITE which is part of the Vanilla 1.0
package (http://users.ox.ac.uk/~strimmer/vanilla/) which in turn relies on
PAL to do its job.

Apart from removing constant or non-informative sites REWRITE can be used
to drop sites with gaps, reformat the alignment nicely in a variety of
formats, jumble the input order of the sequences and even bootstrap the

I note that the version of Vanilla on the web page is still v0.9 but
simultaneously with the release of PAL 1.0 (mid-July) I will put the
new version of Vanilla on the net.

Best regards,


Korbinian Strimmer                  http://users.ox.ac.uk/~strimmer
Dept. of Zoology, Univ. of Oxford, South Parks Road, Oxford OX1 3PS
+44 1865 271272 (phone), -49 (fax), korbinian.strimmer at zoo.ox.ac.uk

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