Commit 2753883b authored by smoretti's avatar smoretti
Browse files

Add extra information file for distribution

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@7177 95c5a404-1f88-0410-a6b0-c3f062b6f34a
parent 712b59e0
FastCodeML has been coded by Mario Valle (mvalle@cscs.ch). This software has been developed in the HP2C Selectome project (http://www.hp2c.ch/projects/selectome/) by Marc Robinson-Rechavi, Nicolas Salamin, Heinz Stockinger (principal investigators) and Hannes Schabauer (project staff) at the University of Lausanne. Please contact marc.robinson-rechavi@unil.ch for inquiries.
Parameter optimizers other than "-m 22" are untested and might not converge properly.
FastCodeML 1.1.0:
- Few corrections to accept pipe character also in sequence names
- New option to fixed branch lenghts (-bl)
- New option fo manage easily number of threads (-nt)
- Codeml optimizer is by default (-m 22)
- Show branch lengths in default output
- Show p0/p1/p2a/p2b & w0/kappa in default output
- Display a warning if tree is rooted
- Display FastCodemL version
FastCodeML 1.0.1:
- Added text files for LICENSE etc. Source files remain unchanged.
- Version 1.0.1 contains additional information files, the sources are
unchanged with respect to 1.0.0.
FastCodeML 1.0.0:
- Initial release
Versions:
1.1.0
- Few corrections to accept pipe character also in sequence names
- New option to fixed branch lenghts (-bl)
- New option fo manage easily number of threads (-nt)
- Codeml optimizer is by default (-m 22)
- Show branch lengths in default output
- Show p0/p1/p2a/p2b & w0/kappa in default output
- Display a warning if tree is rooted
- Display FastCodemL version
This file is part of FastCodeML. FastCodeML is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
FastCodeML is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
However, if you find this software useful for your scientific publication, please cite
M. Valle, H. Schabauer, C. Pacher, H. Stockinger, A. Stamatakis, M. Robinson-Rechavi, N. Salamin
"Optimisation strategies for fast detection of positive selection on phylogenetic trees"
published in Bioinformatics, Oxford University Press (2014).
We thank Sébastien Moretti and Walid Gharib for providing test datasets and feedback on FastCodeML.
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