jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision theory method (DT). It also provides estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged tree topologies. jModelTest 2 includes High Performance Computing (HPC) capabilities and additional features like new strategies for tree optimization, model-averaged phylogenetic trees (both topology and branch lenght), heuristic filtering and automatic logging of user activity.
To run jModelTest from the command-line load the jmodeltest module and use the '
jmodeltest' command in place of
'java -jar jModelTest.jar' command specified in the manual. You can use the jar file directly if you want, of course. It's located at
$HPC_JMODELTEST_DIR/jModelTest.jar. Make sure to use the '
-tr X' option where 'X' is the number of threads to use. The default is 8. Make sure your job script requests appropriate number of computing cores with the '#PBS -l nodes=1:ppn=X'.
To run a short interactive jModelTest session use the gui.rc.ufl.edu machine.