Phylogenetics & Phylogeography Practical(Advanced Analytical Methods)
Practical session with Dr Sam Lycett, March 2015.
(Recommended Youtube playback settings for the best viewing experience: 1080p HD)
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Content:
1. Data Set & Tasks for Practical
- HPAI H5N1 data set
- 92 sequences from 2003 – 2014
- Domestic-galliformes, Domestic-anseriformes, Wild-anseriformes
- Asia, Africa, Europe
2. Tasks (broadly)
- Check Clock-like behaviour using Path-o-gen
- Set up BEAST analysis using BEAUTi
- Diagnose BEAST MCMC output in Tracer
- Make tree figures using FigTree
- Plot spatial-trees using SPREAD
3.General notes
- Keep an electronic log book (e.g. Word document) of what you have done
- including settings
- results figures
- Answers to questions and own observations (this is for your own benefit when you come back to it in 6months time.. )
