HR	Homologous recombination
NHR	Non-homologous recombination
HGT	Horizontal gene transfer
LGT	Lateral gene transfer
SSAPs	Single-strand annealing proteins
SSA	Single-strand annealing
ARGs	Ancestral recombination graphs
MLST	Multilocus sequence typing
CGP	Coarse-graining approach for phylogenetic reconstruction
CRM	Constant relative mutability
SI	Synteny index
PRRSV	Porcine reproductive and respiratory syndrome virus
GPSCs	Global pneumococcal sequence clusters
SNPs	Single nucleotide polymorphisms
HMM	Hidden Markov model
TDA	Topological data analysis
MCMC	Markov chain Monte Carlo
tARG	Topological ARG
OGFs	Orthologous gene families