jMODELTEST 0.1.1 README

10 April 2008

Purpose

jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. The file jModelTest.0.1.pdf includes detailed documentation, and the user is strongly advised to read it carefully before using the program. Please also check the jModelTest Frequently Asked Questions at darwin.uvigo.es.

Software requirements

Operative systems

Although jModelTest it is optimized for MacOS X, executables are provided to run the program under Windows XP and Linux.

Java Virtual Machine (JVM)

To test your JVM, go to http://javatester.org/version.html, or in a console prompt (or terminal window) type "java -version".

The JVM is included also in on the Java Runtime Environment (JRE) or the Java 2 Platform Standard Edition (J2SE). More information on obtaining the JVM at http://java.sun.com. To automatically download the JVM at http://java.sun.com/webapps/getjava/BrowserRedirect

The latest Java versions succesfully tested with jModelTest were:

Download and Installation

Download the package from darwin.uvigo.es and unzip it. You should now see a folder called jModelTest 0.1 package. Note that the original zip file was made on a mac, so in windows or linux you might see some strange files, that start with "." or "-". These are macintosh hidden files, which can be safely removed without affecting the software.

How to start jModelTest

Either double click on the jModelTest.x.x.jar.file, orif this does not work, open a console prompt, move to the jModelTest folder and type "java -jar jModeltest.0.1.jar".

Citation

Posada D. In press. jModelTest: Phylogenetic Model Averaging. Molecular Biology and Evolution.

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 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

David Posada - dposada@uvigo.es