Modeltest 3.7 readme (June 2005)
Updates
The major change in this update is the addition of the Bayesian Information Criterion (BIC). Several other minor changes have also been completed.
- The program calculates now the BIC, BIC differences and BIC weights (approximate posterior probabilities for models). These BIC weights can be use to obtain model averaged estimates and parameter importances.
- The program calculates now pinv(IG) instead of pinv (I+IG), and alpha(IG) instead of alpha (G+IG). Thanks to Roman Biek for pointing that out. Now this
is congruent with Posada and Buckley (2004).
- The program reports now the confidence level for the LRTs.
- Minor aesthetic changes.
- In the comments of the AIC PAUP* block it was printing the name of the hlRT model instead of the name of the AIC model.
- Removed AICcalc function (option "-i).
- Removed AICfile function(option "-f).
- An executable for MacOS 9 is now provided.
Executables
- Mac: compiled executable binaries for MacOS 9 and MacOS X are provided inside the "bin" folder.
- Win: a compiled executable binarie file for Windows (runs in DOS) is provided inside the "bin" folder.
- Unix-like: For Unix-like environmentes, a makefile and source code is provided in the "source" folder (go to this folder and type "make" for compilation)
Quick instructions
The input of Modeltest is a set of likelihood scores corresponding to the specific data set and each one of 56 models. The easiest way of obtaining these scores from an alignment of DNA sequences is using PAUP*. A block of commands for PAUP* is provided below in the file "modelblockPAUPb10) inside the paupblock folder. Follow these steps:
- Open your data file and execute it in PAUP
- Open the command file ("modelblockPAUPb10) and execute it
- PAUP* starts to work in the data following the commands. Once is finished you will see a file called "model.scores" in the same directory as the command file. It is useful to change the name of this file to "yourdataname.scores".
- Run the file "yourdataname.scores" through Modeltest. This is done in a Macintosh just double-clicking in the application provided. However, in PC's you have to run Modeltest through the command prompt (DOS window).
Alternatively, if you are familiar with PAUP*, you can add the PAUP* commands after your data block directly in your data file and execute it.
It is highly recommended to read the documentation!
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 (dposada@uvigo.es) June 21, 2005