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Re: Confusion about RAxML versions and copyright

Hi Andreas,

Still working on it, by the way, are there any Pthreads specialists on this list?

If not here you might be lucky on debian-devel list - but you should
mention the relation to Debian packaging - just in case people wonder
why you are locking for general help ...

Thanks :-)

It might perhaps be a good idea to also integrate CopyCat which is a java-based GUI that implements and steers the whole AxParafit-analysis pipeline into Debian-Med.

See: http://www-ab.informatik.uni-tuebingen.de/software/copycat/welcome.html

Thanks for the description of AxPcoords and this hint.  I added both to
our prospective packages list, but unfortunately the later one seems
to be non-free (regarding DFSG).

That will make the whole thing more comprehensive and easier to use.

Perhaps we could sort out the license issue for our users.

Probably we can, I have put my friends from Tuebingen on the CC.

Markus, Jan and Alexander: would it be possible to resolve the licence issue, such that
CopyCat can become part of the debian-med distribution. Since AxParafit and AxPcoords will
be integrated into debian-med, it really makes sense to ship CopyCat along with that.

Just send an email to Andreas if you are okay with that.

To Alexandros: We are currently working on a system that replaces
our statical todo list in the Debian-Med webspace by a dynamic list
but this is not yet finished and thus the text above will not be
visible for the next weeks but we hope to get it ready in the
beginning of next year.

All right, thanks,

Thanks to david this is done now and oyu can find AxParafit listet at


Any hints for enhancing the description are welcome.  The other
both mentioned above will be listed as soon as the cron job processed

It looks good, thanks David and Andreas.

I would just change the AxPcoords text to:

AxPcoords is a fast, LAPACK-based implementation of DistPCoA (see  http://www.bio.umontreal.ca/Casgrain/en/labo/distpcoa.html)
which is another program by Pierre Legendre, it conducts a principal  coordinates analysis. This program is required for the pipeline
that conducts a full host-parasite co-phylogenetic analysis in combination with AxParafit.

We also have two freely accessible web-servers available for RAxML now, don't know if you want to include that
in the RAxML description:


Happy new year,


Dr. Alexandros Stamatakis

Postdoctoral Researcher
High Performance Computing Bioinformatics

Swiss Federal Institute of Technology
School of Computer & Communication Sciences
Laboratory for Computational Biology and Bioinformatics (LCBB)
CH-1015 Lausanne, Switzerland

Tel:   +41 21 69 31392 (Office)
       +41 796115849   (Mobile)
Skype: stamatak
Email: Alexandros.Stamatakis@epfl.ch
WWW:   icwww.epfl.ch/~stamatak

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