Fig. 1
From: DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference
A phylogeny split into between- and within- cluster components. Sequences C01-1 and C01-2 belong to cluster 1, while C02-1, C02-2, and C02-3 belong to cluster 2. Sequence S01 is a singleton, that is, a cluster of size 1, and O is an outgroup, used to root the sample phylogeny. The red sub-phylogeny is called the between-cluster phylogeny, while the blue sub-phylogenies are called the within-cluster phylogenies