Using IQTREE I received the most optimum models for my data to analyse phylogenetic tree-reconstruction. IQTREE is able to use, aside from the Gamma distribution for heterogeneity across sites also the FreeRate model:
"FreeRate model (Yang, 1995; Soubrier et al., 2012) that generalizes the +G model by relaxing the assumption of Gamma-distributed rates. The number of categories can be specified with e.g. +R6 (default 4 categories if not specified). The FreeRate model typically fits data better than the +G model and is recommended for analysis of large data sets."
Does anyone know if it is possible to use this FreeRate model in MrBayes (or in RevBayes), and if yes, how to I put that in the script?
Hey Pepijn! I came across this problem too. It seems it's not possible to include FreeRate model in mrbayes. Here's a link to another answer:
https://groups.google.com/forum/#!searchin/iqtree/mrbayes$20free$20rate%7Csort:date/iqtree/Yz5y1gUTucA/oVDdcmoOBAAJ
There's a cool parameter in IQTRee '-mset mrbayes' that will only include models also available in mrbayes when doing model testing. It only work with nucleotide data though so if you have something like PICS-Ord regions in your alignment you'll get an error.
Theo Llewellyn yes, I have used that option before, but I think I ended up with the FreeRate anyway. Do you have any idea whether it is possible in RevBayes? And is yes, how to model that?
Don't know about RevBayes sorry. I don't remember them discussing it in the RevBayes tutorials or docs :(
Theo Llewellyn on github I got this answer for RevBayes: https://github.com/revbayes/revbayes/issues/79
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