Difference between revisions of "JModelTest"

Revision as of 20:28, 13 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 -tr X wrapper 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.

@@ Line 39: / Line 39: @@
 <!--Run-->
 {{#if: {{#var: exe}}|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+To run jModelTest from the command-line load the ''jmodeltest'' module and use the <code>jmodeltest -tr X</code> wrapper 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.
 |}}
 <!--PBS scripts-->