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README.md

jmodeltest2

jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision theory method (DT). It also provides estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged tree topologies. jModelTest 2 includes High Performance Computing (HPC) capabilities and additional features like new strategies for tree optimization, model-averaged phylogenetic trees (both topology and branch lenght), heuristic filtering and automatic logging of user activity.


Download

Check 'releases' section for the latest distributions.

New revisions of jModelTest will also be hosted in google drive: https://drive.google.com/folderview?id=0ByrkKOPtF_n_OUs3d0dNcnJPYXM#list


NEWS!

03/03/2016 - New revision fixed bug with equal taxa name prefixes. Fixed minor bugs.

20/02/2015 - New revision Fixed minor bug in console version. NNI tree search operation was taken as default for ML starting tree, instead of BEST.

20/11/2014 - New revision Fixed some bugs with Windows OS

03/09/2014 - New revision Added --set-local-config and --set-property arguments.

26/08/2014 - New revision Fixed bug with -O argument (hypothesis order for hLRT).

06/08/2014 - New revision Added checkpointing feature and confirmation on run cancel.

05/04/2014 - New revision Added PAUP* block to log files. Fixed bug with DT criterion. Check the whole revision updates at the wiki.

05/06/2013 - New revision Fixed bug with PAUP* block. Added argument for forwarding standard output to a file.

03/01/2013 - New revision Fixed bug with paths including whitespaces. New binaries distribution also includes updated PhyML binaries with a much better performance.

01/08/2012 - The jModelTest paper has been published: Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772. Although the main text is quite short, it comes with 15 pages of supplementary material!


Citation

When using jModelTest you should cite all these:

Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9(8), 772.

Guindon S and Gascuel O (2003). A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood". Systematic Biology 52: 696-704.


Discussion group

Please use the jModelTest discussion group for any question: http://groups.google.com/group/jmodeltest


Disclaimer

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 3 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. The jModelTest distribution includes Phyml executables.

These programs are protected by their own license and conditions, and using jModelTest implies agreeing with those conditions as well.