RAxML 7.1.0 (alpha) available
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- Subject: RAxML 7.1.0 (alpha) available
- From: Alexandros Stamatakis <stamatak@in.tum.de>
- Date: Thu, 12 Mar 2009 15:40:48 +0100
- Message-id: <49B91EF0.3000903@in.tum.de>
- Reply-to: stamatak@cs.tum.edu
Dear Users of RAxML,
You are receiving this message since in the past you have expressed your interest in using RAxML.
If you do not want to receive this information any more please accept my apologies and just send
an empty Email with subject "remove from RAxML-list" to stamatak@cs.tum.edu such that I
can remove you from this mailing list.
RAxML has recently been updated and is now available for download as RAxML-7.1.0 at
http://wwwkramer.in.tum.de/exelixis/software.html
I am still working on an updated Manual so please consult the on-line help
via "raxmlHPC -h".
This is the alpha release, so please expect a lot of bugs, weird program outputs etc.
To report bugs send me an email and please send me all input files, the exact invocation,
details of the HW and operating system, as well as all error messages printed to screen.
The MPI version does not work yet, only Pthreads and the sequential version work.
To compile:
sequential: "make -f Makefile.gcc"
Pthreads: "male -f Makefile.PTHREADS"
New features:
* Improved parallel load balance for Pthreads version when conducting per-partition branch length estimate
* Binary (Morphological) and Secondary Structure models implemented
* Estimate of GTR model of amino acid substitution
* Added LG model of protein substitution
* Computation of RF and WRF tree distances
* Implementation of significantly faster methods to operate on bipartitions of trees
* Implementation of WC and FC Bootstrap convergence criteria, they can be executed on the fly or a posteriori
* For details on the bootstop method see N.D. Pattengale, M. Alipour, O.R.P. Bininda-Emonds, B.M.E. Moret,
A. Stamatakis: "How Many Bootstrap Replicates are Necessary?". Proceedings of RECOMB 2009 preprint at
http://lcbb.epfl.ch/bootstopping.pdf
* Rapid Bootstraps now feasible under CAT, GAMMA, as well as GAMMA+P-Invar
* Parsimony ratchet implementation
* 4 Algorithms to classify sequences from environmental samples into a given reference tree
(to be described in more detail)
I have fixed various bugs and slightly changed the search algorithms and command line interface.
Comments and suggestions are always welcome.
Best regards,
Alexis
--
Dr. Alexandros Stamatakis, Junior Research Group Leader
The Exelixis Lab
Bioinformatics Unit (I12)
Department of Computer Science
Technische Universität München
Tel: +49 162 8541515 (Mobile)
+49 89 28919434 (Office)
Fax: +49 89 28919414
Skype: stamatak
Email: stamatak@cs.tum.edu
WWW: http://wwwkramer.in.tum.de/exelixis/
Room: 01.08.061
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