These are written for use with jModelTest 2.1.4 running on a Mac
File->Load DNA Alignment and select alignment of interest
You can try this example file.
Analysis->Compute likelihood scores
To run a very quick analysis, just choose
Likelihood settings
- Number of substitution schemes->3
- Base frequencies->check
- Rate variation->uncheck both +I and +G
- Base tree for likelihood calculations->Fixed BIONJ-JC
and then click "Compute likelihoods"
To include the GTR model in the scheme you need to run as above but using Base frequencies->check
For now we'll just use AIC
Analysis->Do AIC calculations...
then click "Do AIC calculations"
Results->Show results table
Then choose the AIC tab.
The preferred models are those with the lower AICs; used very naievely, one would assume that the best model to take is the one with the lowest AIC.
Results->Build HTML log
will write an HTML output file containing the results of the analysis