Fig. 2
From: TreeToReads - a pipeline for simulating raw reads from phylogenies
Input and inferred trees for two case studies, Salmonella enterica Bareilly and Listeria monocytogenes. Variable sites called for Salmonella enterica Bareilly by mapping reads to the anchor genome as a reference (close reference), and to a reference genome outside of the sampled tree (distant reference). Listeria monocytogenes reads were mapped to the anchor genome