Phyml
Phyml
http://www.atgc-montpellier.fr/phyml
Phylogenetic estimation using Maximum Likelihood
PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test).
PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the “comfort zone” for PhyML generally lies around 3 to 500 sequences less than 2,000 character long.
This pakcage also includes PhyTime.
Licensing
License
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License
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License: mixture
mixture In my understanding, the text (GPL-2+) is only aggregated with the font (OFL-1.1) and the PostScript code (psfrag). CP,
2011-06-26.License
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License: install-sh
install-sh Permission to use, copy, modify, distribute, and sell this software and its documentation for any purpose is hereby granted without fee, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation, and that the name of M.I.T. not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. M.I.T. makes no representations about the suitability of this software for any purpose. It is provided
"as is" without express or implied warranty.
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License: gpl-2+
GPL-2+ This program 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 2 of the License, or (at your option) any later version.
This program 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.
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
02110-1301 USA.
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Debian: Andreas Tille <tille@debian.org>
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License: gpl-2+ GPL-2+ (see above)
License
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Debian: Andreas Tille <tille@debian.org>
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5 August 2013
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License: gpl-2+ with autoconf exception
GPL-2+ with Autoconf exception This program 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 2, or (at your option) any later version.
This program 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.
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
As a special exception to the GNU General Public License, if you distribute this file as part of a program that contains a configuration script generated by Autoconf, you may include it under the same distribution terms that you use for the rest of
that program.
Leaders and contributors
Resources and communication
| Audience | Resource type | URI |
|---|---|---|
| Download | http://phyml.googlecode.com/files/phyml-20120412.tar.gz | |
| Debian (Ref) | https://tracker.debian.org/pkg/phyml |
Software prerequisites
Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the page “GNU Free Documentation License”.
The copyright and license notices on this page only apply to the text on this page. Any software or copyright-licenses or other similar notices described in this text has its own copyright notice and license, which can usually be found in the distribution or license text itself.