[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Re: Confusion about RAxML versions and copyright

Hi Andreas,

First of all I would like to wish you a happy new year.

Yes, I am currently working on it, you should get an email regarding this
hoepfully soon.


Still working on it, by the way, are there any Pthreads specialists on this list?
We made a transition from OpenMP to Pthreads for one of the parallel versions to have
better control over the machine, and would need some advice on optimizing it further.

Yes, that is correct, if I am not seriously mistaken I already added a GPL
license to the source code following you inquiry.

Shame on me - I should have checked the source and not only the web
page.  The source contains a file GPL_RAxML.txt.

Don't worry.

BTW, if you are working on a new version I have some minor and rather
aesthetical request:  The source code would look better if you would
not set execute permissions on all files and many source files are
upper case.  This looks - hmmm, how to say - WindowIsh ;-)

I just checked, neither is the case any more in the new release,
I don't want to be accused of writing windowish code ;-)

There is if you go to this page http://icwww.epfl.ch/~stamatak/AxParafit.html

"Manual, Source Code (under GPL), and Binaries"

Here I did the other non working approach for finding the license:
I ignored the "(under GPL)" string and just looked at the source
archive. ;-)
Sorry for the noise, but adding it to the code (in a next release)
would be very reasonable.

Sure, I will do that.

Thanks for integrating my programs into debian-med.

Well, it's not yet done.  We are just doing the first steps into
this direction which is listing it as prospective package.  For
Debian-Med readers I added the following chunk to tasks/bio:

Depends: raxml
Homepage: http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm
License: GPL
Pkg-Description: Randomized Axelerated Maximum Likelihood
 RAxML is a program for sequential and parallel Maximum Likelihood-based
 inference of large phylogenetic trees. It has originally been derived
 from fastDNAml.

Depends: axparafit
Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
License: GPL
Pkg-Description: optimized statistical analysis of host-parasite coevolution
 AxParafit is a highly optimized version of Pierre Legendre's Parafit
 program for statistical analysis of host-parasite coevolution.
 AxParafit has been parallelized with MPI (Message Passing Interface)
 for compute clusters and was used to carry out the largest
 co-evolutionary analysis to date for the paper describing the software.

It will show up in SVN tonight.  I'm a little bit unsure about the
description of AxPcoords.  In how far are AxPcoords and AxParafit
are different and how I could find a reasonable short and long

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.

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

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

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,


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

Reply to: