Course development notes

[tavareshugo]

We can keep this course short (1-day), covering only some general/basic concepts in phylogeny:

• What is a phylogeny
• MSA
• Phylogenetic inference
• Tree uncertainty (bootstrap)
• Bayesian inference (BEAST/BEAuTi) - 3h dedicated to this section
  • simple tree inference - alternative method to ML for tree inference (to get branch uncertainty)
  • timed trees or possibly Skyline methods

In terms of datasets:

• The main dataset will be SARS-CoV-2 with time of collection (and possibly geography) metadata. This will be used both for ML and Bayesian section
• Other datasets for the ML part could include:
  • primate mtDNA (original course), hominid mtDNA, etc...

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Separately, we will then have follow-on courses, such as:

• Bacterial genomics
• Phylogenomics

[tavareshugo]

Some tasks (for March 2023 catch-up):

• [x] (Nicola) Get SARS-CoV-2 data to use throughout the practical
• [ ] (Hugo) Get other smaller example data prepared:
  • primate mtDNA (from the original course)
  • hominid mtDNA - Denisovan; Neanderthal; modern human
  • Darwin's finches
• [ ] (Hugo) Edit materials

[tavareshugo]

Working timetable:

09:30 - 10:30 -- General intro 10:30 - 11:30 -- MSA 11:30 - 12:30 -- tree inference (distance-based and parsymony and ML slides) 12:30 - 13:30 -- Lunch 13:30 - 14:30 -- tree inference with ML (practical) 14:30 - 15:00 -- bootstrap 15:00 - 16:30 -- Bayesian tree inference 16:30 - 17:00 -- Additional BEAST applications (e.g. phylogeography or dating or something else) introduced only as slides - maybe some bonus exercises for more advanced users

Information needed before pilot run of workshop on the 28th Jun:

• [ ] Data
• [x] Software requirements