Hello,

You could try PartitionFinder.

regards,

Sebastian

You can use alternatively the MEGA software for model selection. It uses BIC and AIC as well. http://www.megasoftware.net/

Have a look at the advanced model test in iqtree - it's a ML based program, but the free-rate model selection tool it has might be useful to you.

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.

Please try some analysis using rstudio and rserver. Download it from the link and search for the packages for this program like ape(analysis of phylogenetics & evolution) and phangorn by opening rstudio. https://www.rstudio.com/