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Mac users will be given a choice to install the command-line version of PAUP. as well as the classic Mac GUI version. Work is currently underway to “carbonize” the GUI Mac version of PAUP.; however, at this time, we cannot speculate on when this version will be available.

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.

Paup Manual

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Last updated 22 February 2007 • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •? • Why are all the answers given in terms of commands and not menu choices?

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Primarily this is to maintain consistency. All versions of PAUP* have a command line interface, whereas only a few versions have a menu system, thus if answers were given in terms of menu choices, users of the UNIX and DOS versions would be out of luck. Also, many users prefer to put all of the commands for a particular analysis in a PAUP block directly in the data file itself. This maintains a complete record of how the analysis was carried out, which is useful later for purposes of writing the “Methods” section of a paper.

The commands presented here can all be used within PAUP blocks as well as on the command line itself, thus facilitating the creation of PAUP blocks. () If I don’t find it here, does that mean that it doesn’t exist? This FAQ is written as the need arises, and thus it will continue to grow in completeness each week. Thus, this FAQ is not intended to be a replacement for the PAUP* manual, but we hope it is a useful surrogate until the program and manual are officially published. The FAQ’s authors frequently receive questions (usually by email) about using PAUP*, and this provides a convenient mechanism for responding to common questions that we receive over and over again. Please feel free to candidate questions for inclusion in the FAQ. () Can I submit questions that I think should be part of this FAQ?

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We welcome submission of candidate questions for the PAUP* FAQ, but be aware that the decision to include any particular question resides with the authors of the FAQ. The questions most likely to make it into the FAQ are those that we feel would benefit a large proportion of PAUP* users.