Removing constant sites from alignment
imbam at po.uni-stuttgart.de
Wed Aug 9 11:00:33 EST 2000
I had also the same questions. I will use your advise.
For Kristo and Nicolas, have you already succeeded?
Korbinian Strimmer wrote:
> 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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