Cryptic transmission of SARS-CoV-2 in Washington State

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).