Constructing phylogenetic trees in BEAST package and MrBayes requires an AIC selected best-fit substitution model. Running a model search in mrmodeltest requires a script created in PAUP.
You can use alternatively the MEGA software for model selection. It uses BIC and AIC as well. http://www.megasoftware.net/
Hello Juan,
I think IQTree is the most comprehensive phylogenetic model tester currently. It is also easy to use and has a well-written manual.
If you want to test by Bayesian cross-validation this can be done under PhyloBayes. However, on reasonable sized matrices you'll need a lot of computation power, or a lot of time on your hands :)
If you want to go quick-n-dirty without model testing, just apply Le & Gascuel (LG), plus a gamma distribution on rate. For multicellular nuclear sequence data, LG is very often best fit. This will not be true for other types of data, particularly epidemiological data.
Best regards,
Al.
http://www.iqtree.org/
http://megasun.bch.umontreal.ca/People/lartillot/www/downloadmpi.html
Thank you everyone for the splendid suggestions, much obliged indeed.
- Badges
- Science topic
- Similar topics
- Biological Science
- Evolutionary Biology
- Phylogenetics