MOTMOT (Models Of Trait Macroevolution On Trees is an R package for fitting various models of evolution to data on phylogenies and species traits. The paper describing the package is free to download from Methods in Ecology and Evolution. The package is not currently available on CRAN but can be downloaded or installed directly from github. Installation is (usually) straightforward with the following commands:

> library(devtools)
> install_github("ghthomas/motmot")


PASTIS (Phylogenetic Assembly with Soft Taxonomic InferenceS) is another R package. It is simply a set of functions to generate MrBayes input files with soft taxonomic constraints as first described in Jetz et al. 2012. The package is available from CRAN and a short (freely available) software paper describing its functionality is available here.

A bright motmot was acting quite rowdy
weaving and squawking quite rowdy
this “pastis is delis”
he burped with a sneeze
“but why is everything suddenly cloudy”

– Arne Mooers