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 ) ********************************* 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 ?
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