Jmodeltest2
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.
License
This program is a free software, freely available to all users under GNU GPLv3
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of jmodeltest and load default version of jmodeltest as
module avail jmodeltest/ # list available modules module load jmodeltest # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail jmodeltest
and choose explicit version you want to use.
There is defined alias jmodeltest-2.1.10 which points to the program jar file. Example of running:
java -jar /software/jmodeltest2/2.1.10/dist/jModelTest.jar
If you do not need to set any special parameters to java, you can use the available alias to the above command called jmodeltest-2.1.10.
jmodeltest-2.1.10 -help
Documentation
Documentation is in the folder /software/jmodeltest2/2.1.10/manual