Special features of phangorn (Version 2.0.0)

This document illustrates some of the phangorn [3] specialised features which are useful but maybe not as well-known or just not (yet) described elsewhere. This is mainly interesting for someone who wants to explore different models or set up some simulation studies. We show how to construct data objects for different character states other than nucleotides or amino acids or how to set up different models to estimate transition rate. The vignette Trees describes in detail how to estimate phylogenies from nucleotide or amino acids.