Phylogenetics & Phylogeography Practical(Advanced Analytical Methods)
Practical session with Dr Sam Lycett, filmed at The Roslin Institute, March 2015.
(The recommended YouTube playback settings for the best viewing experience is 1080p HD )
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Content:
Part 2: Set up a BEAST analysis
- Make XMLs with BEAUTI
- plain - SRD06, relaxLn, constPop with
- clock rate prior = normal(mean=4e-3,std. dev=4e-3), range 0-0.1
- CP1+2,3 priors uniform 0-100

With traits:
- Host trait, and Region trait (separately), using asymmetric model
- Latitude and Longitude, using 2 part continuous trait and brownian motion model
- Start the “plain” XML in BEAST (to check it runs)
- The completed runs are supplied – look at the *_screen_output.txt files; how long did they take ?