MrModeltest 2.3 README, May 22 2008
MrModeltest 2.3 by Johan A. A.
Nylander, Dept. Systematic Zoology, EBC, Uppsala University, Sweden.
For performing hierarchical likelihood ratio tests and calculating
approximate AIC and/or very approximate AICc values of the nucleotide
substitution models currently implemented in both PAUP*4 and
MrBayes v3. Version 2.3 also does some model averaging of the parameter
estimates obtained by PAUP.
MrModeltest 2.3 is a modified version of David Posada's Modeltest 3.6
homepage). "Modified version" means that it was rewritten to
compare 24 instead of 56 models of nucleotide substitution (basically a
Modeltest version 1.0). On the other hand, all of the 24 models can be
implemented in MrBayes version 3. Furthermore, MrModeltest uses (by
default) four different hierarchies for the likelihood ratio tests. The
hierarchies are described in detail in Posada, D. and K. A. Crandall.
2001. Selecting the best-fit model of nucleotide substitution.
Systematic Biology, 50:580-601 (Fig. 4a-d). The hierarchies implemented
in MrModeltest are also depicted in the files 'hLRT1.jpg',
Nylander, J. A. A. 2004. MrModeltest v2. Program distributed by the
author. Evolutionary Biology Centre, Uppsala University.
Installing the pre-build program on Windows or MacOSX
1. Unpack the distribution
2. Find the appropriate binary file for your operating system and
use directly (see Running MrModeltest2 below) or,
preferrably, copy it to a location included in your PATH.
Note: The windows version is compiled and tested on WinXP.
Installing from source (on UNIX/MacOSX)
1. Unpack the distribution:
2. cd into the distribution directory:
Note for MacOSX users:
The tools for compiling C code are not installed by default on MacOSX
(at least not for v.10.3.7). Therefore, there should be a precompiled
binary in the MrModeltest2 distribution for you to use. See step 4
I do recommend, however, to install the necessary tools and compile the
code on your own system. For OS v. 10.3.7, the tools can be installed
from the Mac OS X Install Disc 1, directory Xcode Tools. Then proceed
with step 3 below.
3. Compile by typing:
4. The binary file 'mrmodeltest2' can then be run in the same directory
or be moved somewhere on your system where you have access to it (i.e.,
in your PATH).
Installing as deb package
The deb package in MrModeltest2.3/deb was created using
checkinstall on Ubuntu Linux 7.10 64bit Intel version. It can be
installed (in /usr/local/bin) by using command:
sudo dpkg -i mrmodeltest2_2.3-1_amd64.deb
and uninstalled by using
sudo dpkg -r mrmodeltest2
Before using MrModeltest2
1. Execute your data file in PAUP*.
2. Execute the file 'MrModelblock' in PAUP*.
A file called 'mrmodel.scores' will appear in the current directory.
3. This file is the input for MrModeltest2.
MrModeltest2 does not have a graphical user interface.
Therefore, UNIX/Win/MacOSX users need to open a terminal
("Console","DOS window") and type:
mrmodeltest2 < mrmodel.scores > out
The results are written in the 'out' file.
Note: If mrmodeltest2 is not in your PATH, you can try to run the
program by first cd in to the same directory where the binary and the
mrmodel.scores are located and then type:
./mrmodeltest2 < mrmodel.scores > out
MacOS Classic users:
Note: as from version 2.3, I do not longer have access to a
compiler for MacOS9. This distribution is now no longer distributed. The instructions below are for version 2.2.
1. Double click on the 'MrModeltest2.2' application.
2. Click on the left-hand 'File' button. Choose the 'mrmodel.scores'
file and click 'Ok' (or 'Open').
3. Click on the right-hand 'File' button. Click 'Ok' (or 'Save').
4. Click 'Ok' to run and choose 'Quit' and 'Don't save' to quit.
The results are written in the 'MrModeltest2.2.out' file.
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.