phyTreeFromTransTree
phyTreeFromTransTree downsamples a complete transmission tree (provided as an edgelist of who infected whom and when) into a bifurcating phylogenetic tree.
The main function is samplePhyloTree.m, and you can step through a demo with buildExample.m. Pretty plots are generateed using ggplotPhyloTree.R (which can be called from the command line or with a matlab wrapper).