Software: Modelgenerator

Thomas Keane thomas.m.keane at MAY.IE
Mon Dec 13 08:07:38 EST 2004


Hi,
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

Cheers,
Thomas

Posada, D. and Crandall, K.A. (2001) Selecting the Best-Fit Model of
Nucleotide Substitution, Systematic Biology, 50(4), 580=96601

--=20
Thomas Keane,
Bioinformatics and Pharmacogenomics Lab,
Department of Biology,
National University of Ireland,
Maynooth,
Ireland.

http://www.cs.may.ie/distributed
http://www.cs.may.ie/~tkeane

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

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