jModelTest2

jModelTest is used 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 length), heuristic filtering and automatic logging of user activity. jModelTest2 on XSEDE submits jobs to Exanse, a large NSF XSEDE Resource. Each job is assigned to 8 cores, which can speed up the results signficiantly relative to the serial version. Manual for jModelTest2: here. jModelTest2 Google group: https://groups.google.com/forum/#!forum/jmodeltest

 

jModelTest home page here.

INPUT = dna matrices in several formats. The native format for PhyML (used as part of jModelTest2 runs) is Phylip.

Simple Example of Run Input/Output

Input File Type	File Name
input file	infile.phy
Output File Type	File Name
log file	outfile.txt

Known Issues:

• No known issues.

If there is a tool or a feature you need, please let us know.