README file for MrAIC.pl 1.4.6 -- 2014-June-02

MrAIC.pl 1.4.6 by Johan A. A. Nylander

E-mail: jnylander @ users.sourceforge.net

See also: https://github.com/nylander/pMrAIC

MrAIC.pl is a Perl script for calculating AIC, AICc, BIC, and Akaike weights (for a review, see Burnham and Anderson, 2002) for nucleotide substitution models. Likelihood scores under different models are estimated using PHYML (Guindon and Gascuel, 2003).

Input is DNA data in PHYML format (see below).

If the argument -modeltest is parsed, 56 models (the ones tested in Modeltest [Posada and Crandall, 1998]) are evaluated in PHYML. Default is to test the 24 models that can be specified in MrBayes v3 (Ronquist and Huelsenbeck, 2003). These are JC, F81, K2P (aka K80), HKY, SYM and GTR, each combined with Propinv (I) and/or Gamma (G).

A difference between Modeltest and MrAIC.pl is that MrAIC.pl does not evaluate all models on the same, approximate topology. Instead, PHYML is used to try to find the maximum of the likelihood function under all models. This is necessary for finding AIC, AICc, or BIC for the models.

1. Perl must be installed on your system.

2. PHYML (Guindon and Gascuel, 2003) version 3 must be installed on your system (named "phyml" and be in the PATH). Alternatively, user might edit MrAIC.pl to specify the full path to the PHYML binary.

Windows users: Make sure you have set the environment variables to include an executable named "phyml.exe". Alternatively, rename/copy/link the phyml_w32.exe to phyml.exe and put it in the same folder as the mraic.pl script.

Interactively or by passing arguments as below

mraic.pl infile
mraic.pl -modeltest infile

where infile contain DNA data in PHYML format which is somewhat similar to the PHYLIP format (see example files dat.txt and dati.txt). Example, "sequential" format (note the space between taxon name and sequence):

3 8
Taxon_1 ACGTACGT
Taxon_2 ACGTACGT
Taxon_3 ACGTACGT

In this script, sample size (n) used in AICc and BIC is assumed to be the number of characters in the data matrix. This is probably not correct when it comes to phylogenetic analyses (Nylander, 2004), but serve as an approximation to the true n. Branch lengths are included when specifying the total number of parameters for the models. AICc values are only printed if the number of parameters are high compared to number of characters (Nchar/Max.Number of parameters < 40). Maximum number of free parameters is 10 (for the GTR+I+G model) plus the number of branch lengths. The limit of 40 is a heuristic suggested by Burnham & Anderson (2002). Furthermore, all calculations of Akaike weights, AIC, AICc, and BIC are all dependent on PHYML's ability to find the maximum of the likelihood under each model. More elaborate searches might be necessary to get more correct assessment of the ML for some data sets!

Thanks to Torsten Eriksson for advice on slick Perl programming.

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

Burnham, K. P., and D. R. Anderson. 2002. Model selection and multimodel inference, a practical information-theoretic approach. Second edition. Springer, New York.

Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate phyogenies by maximum likelihood. Systematic Biology, 52:696-704:

Nylander, J. A. A. 2004. Bayesian phylogenetics and the evolution of Gall wasps. Comprehensive Summaries of Uppsala Dissertations fro the Faculty of Science and Technology 937. Uppsala University.

Posada, D., and K. A. Crandall. 1998. MODELTEST: Testing the model of DNA substitution. Bioinformatics 14:817-818.

Ronquist, F., and J. P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.

Copyright (c) 2004-2014 Johan Nylander

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.