3. Phylogenetics & Phylogeography Practical 2 - Part 1 -

Phylogenetics & Phylogeography Practical(Advanced Analytical Methods)
Practical session with Dr Sam Lycett, March 2015.
(Recommended KZbin playback settings for the best viewing experience: 1080p HD)
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Content:
Practical 2 - part 1: 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 ?

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