I ran ProtTest3.0 using my alignment of viral protein sequences. I tested all available models, and the best ones were MtMam based (they differ in the parameters), an HIV one and only then does JTT appear.
Since I know for sure that the protein isn't mitochondrial, should I use the MtMam based model, since it was the best one for the evolution of this particular protein, or should I ignore this result and skip to the best JTT model (JTT models were better than the LG ones).
In principle that is the model that best fit your data, so I would recommend to use it. May be your viral sequences evolve more like the mitochondrial ones used to derive the MtMam model than those used in other models.
In any case it is never a bad idea to check the results with other models.
- Badges
- Science method
- Similar topics
- Biological Science
- Evolutionary Biology
- Phylogenetics
- Phylogenetic Analysis