With all the packages (and beta stage groups of functions) for comparative phylogenetics in R (tested here: picante, geiger, ape, motmot, Liam Revell’s functions), I was simply interested in which functions to use in cases where multiple functions exist to do the same thing. I only show default settings, so perhaps these functions would differ under different parameter settings. [I am using a Mac 2.4 GHz i5, 4GB RAM]
Get motmot here: https://r-forge.r-project.org/R/?group_id=782
Get Liam Revell’s functions here: http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/
It’s hard to pick an overall winner because not all functions are available in all packages, but there are definitely some functions that are faster than others.