Ideas for expanding materials

[tavareshugo]

• Timed trees: introduce the concept and how they can be estimated. Could introduce both ML and Bayesian methods. As a practical could just use treetime.
• Typing schemes: introduce MLST, cgMLST, pros and cons.
• Visualisation: additional and/or more advanced phylogeny visualisations using ggtree (but this adds an extra hard prerequisite)

[tavareshugo]

• Lineage assignment and clustering: a larger dataset (maybe starting from preprocessed FASTA files) where fastBAPS can be run. To cover the workflow of generating an initial tree, cluster with fastBAPS, generate reference-based alignments for each cluster, followed by gubbins and iqtree

[tavareshugo]

• Mutational spectra: include Chris' talk in the schedule (and in the future could consider a practical?)

[tavareshugo]

• GWAS - lecture and/or practical with pyseer