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:
Practical 1: Checking clock-like-i-ness
- Create a neighbour joining tree in MEGA, using TN93 model, gamma distribution of rates over sites, and heterogenous rates over lineages
- Save this both in MEGA native format (*.mts) and export to newick format (*.nwk)
- Open this tree in Path-o-gen
- Add time information to the sequences (the date is in the last part of the taxa name)
- Find the best fitting root
- Plot the diversity with respect to time
- What is the estimated clock rate ?