Model Testing

As the "Model Testing" tool can help identify the best substitution model (20.4.1) to be used for "Maximum Likelihood Phylogeny" tree construction, it is recommended to do "Model Testing" before running the "Maximum Likelihood Phylogeny" tool.

The "Model Testing" tool uses four different statistical analyses:

to test the substitution models:

To do model testing:

        Toolbox | Classical Sequence Analysis (Image gene_and_protein_analysis) | Alignments and Trees (Image alignmentsandtrees)| Model Testing (Image model_test_16_n_p)

Select the alignment that you wish to use for the tree construction (figure 20.5):

Image modeltesting_step2
Figure 20.5: Select alignment for model testing.

Specify the parameters to be used for model testing (figure 20.6):

Image modeltesting_step3
Figure 20.6: Specify parameters for model testing.

The output from model testing is a report that lists all test results in table format. For each tested model the report indicate whether it is recommended to use rate variation or not. Topology variation is recommended in all cases.

From the listed test results, it is up to the user to select the most appropriate model. The different statistical tests will usually agree on which models to recommend although variations may occur. Hence, in order to select the best possible model, it is recommended to select the model that has proven to be the best by most tests.