This directory contains helper scripts to aid with common downstream analyses. Each subdirectory contains scripts related to specific step(s) of the FAVITES-Lite simulation workflow.
contact_network: Scripts related to analyzing the contact networktransmission_network: Scripts related to analyzing the transmission networkphylogeny: Scripts related to analyzing the phylogeny (either the time tree or the mutation tree, or both)distances: Scripts related to analyzing distances (either from trees or from sequences)