| Parameter name | Suggestion (for this step) | Default? |
|---|---|---|
| Data type | Amino Acid | |
| Evolutionary model | JTT | |
| Equilibrium frequencies | ML/Model | Yes |
| Proportion of invariant sites | estimated | Yes |
| Number of categories for the discrete gamma model | 4 | Yes |
| Parameter of the gamma model | estimated | Yes |
| Tree topology search | SPR | Yes |
| Optimise parameter | Tree topology, Branch length, Model parameter | Yes |
| Statistical test for branch support | Likelihood aLRT statistics |
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