I developed SA and morph-models packages for BEAST2 phylogenetic software and contributed to BDSKY package. 

SA package (source on GitHubenables trees with sampled ancestors — sampled individuals that lie directly on branches of a phylogeny and represent ancestors of other sampled individuals.  This package also adds the sampled-ancestor birth-death model. The sampled ancestor variant of the skyline birth-death model is in BDSKY package (source on GitHub). Morph-models package (source on GitHub) adds Lewis MK model of morphological evolution.

The packages can be installed from BEAUti user interface (go to manage packages in the menu bar) that comes with BEAST2. 

The relevant tutorials are: