I'm looking for a R Software package to run a Transversion model (TVM + I + G) and Transition model (TIM2 + I + G), but I can't find if there is such a package to do this. Is there a package available to run these models?
Hola Alex,
the phangorn package can estimate these models. The functions you want to look at are called pml and optim. pml . The r-sig-phylo site is probably better for asking questions.
Regards Klaus
Thank you very much Dr. Klaus Schliep! I'll check the site and download the package!
You should download the R program (http://www.r-project.org) first and install the mmSAR package within it.
Thank you Atena Eslami, I actually have R software, just want to know about a package, in this case, I'll download the mmSAR you suggested. Thank you.
Maybe this link can help also:
http://www.r-bloggers.com/transitions-and-transversions-in-r/
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