phylogenetics.qmd

# Phylogenetics {@sec-phylogenetics .unnumbered}

Phylogenetic methods allow us to reconstruct the evolutionary history of, and relationships between, organisms.
Here, we can use these approaches to obtain evidence about the likely order and route of transmission of bacterial isolates in the context of an infection outbreak, such as this study.

In this section, you will construct a phylogenetic tree from the aligned SNPs (single-nucleotide polymorphisms) of a set of isolates from rooms 6, 9, and 11 - and a reference isolate believed to have existed prior to the study.
You will visualise the tree you construct, and use it to propose a potential order of events for infection and transmission in this burns ward.