[BiO BB] Software: Modelgenerator

Thomas Keane thomas.m.keane at MAY.IE
Thu Dec 16 05:59:03 EST 2004

We have just completed the development of a fully self-contained 
substitution model selection application. Modelgenerator supports 28 
amino acid models and 24 nucletoide models (base model with three 
optional rate distributions: Gamma, Invariable sites, and 
Gamma+Invariable sites). Model selection is performed using both the 
hLRT and AIK tests (Posada and Crandall, 2001). We have devised a 
modified hLRT for the amino acid models that has shown to be extremely 
effective in our simulated data tests (manuscript in preparation). Our 
tests have also shown the importance of using Modelgenerator when 
choosing a particular amino acid model - as arbitrarily choosing a model 
can lead to incorrect or suboptimal phylogenies. Unlike other popular 
modeltesting software, Modelgenerator does not require the installation 
of any other software package (e.g. PAUP*).

We invite you to try this application on your datasets and welcome any 
positive or negative feedback on the application.The application can be 
downloaded from: http://bioinf.may.ie/software/modelgenerator


Posada, D. and Crandall, K.A. (2001) Selecting the Best-Fit Model of 
Nucleotide Substitution, Systematic Biology, 50(4), 580–601

Thomas Keane,
Bioinformatics and Pharmacogenomics Lab,
Department of Biology,
National University of Ireland,


E: thomas.m.keane at may.ie
P: +353 1 708 6043
F: +353 1 708 3845

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