Difference between revisions of "JModelTest"

Revision as of 17:56, 18 December 2012

Description

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.

Required Modules

Serial

jmodeltest

System Variables

HPC_{{#uppercase:jmodeltest}}_DIR

Additional Information

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.hpc.ufl.edu machine.

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 <!--Run-->
 {{#if: {{#var: exe}}|==Additional Information==
-To run jModelTest from the command-line load the ''jmodeltest'' module and use the '<code>jmodeltest'</code> wrapper. Make sure to use the '<code>-tr X</code>' 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 jModelTest from the command-line load the ''jmodeltest'' module and use the '<code>jmodeltest'</code> command in place of <code>'java -jar jModelTest.jar'</code> command specified in the manual. You can use the jar file directly if you want, of course. It's located at <code>$HPC_JMODELTEST_DIR/jModelTest.jar</code>. Make sure to use the '<code>-tr X</code>' 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_Programs|gui.hpc.ufl.edu]] machine.