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C program for selecting DNA substitution models using PAUP*
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README.md

MrModeltest2

C program for selecting DNA substitution models using PAUP*.

MrModeltest 2.4 README, Sept 2018

MrModeltest 2.4 by Johan A. A. Nylander. Orignal code by David Posada, U. Vigo, Spain.

E-mail: johan.nylander@nbis.se

Description

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 2.4 also does some model averaging of the parameter estimates obtained by PAUP*.

MrModeltest 2.4 is a modified version of David Posada's Modeltest 3.6 (see Modeltest 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, hLRT2.jpg, hLRT3.jpg, and hLRT4.jpg.

MrModeltest 2.4 are currently only able to read the output from newer ("test") versions of PAUP*. For users with older PAUP* versions (< 4.0a155), version 2.3 should still work as expected.

Suggested reference

Nylander, J. A. A. 2004. MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.

Quick instructions

Installing the pre-build program on Windows or MacOSX

  1. Find the appropriate binary file for your operating system (in the 'bin' folder) and use directly (see Running MrModeltest2 below) or, preferrably, copy it to a location included in your PATH.

Installing from source (See file src/INSTALL)

  1. cd into the distribution src directory:

     cd MrModeltest2/src
    
  2. Compile by typing:

     make
    
  3. 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).

Before using MrModeltest2

  1. Execute your data file in PAUP*:

     exe datafile.nex;
    
  2. Execute the file MrModelblock in PAUP*. A file called mrmodel.scores will appear in the current directory. This file is the input for mrmodeltest2.

     exe MrModelblock;
    

Running MrModeltest2

MrModeltest2 does not have a graphical user interface. Therefore, UNIX/Win/MacOSX users need to open a terminal ("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

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.

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