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Practical 3 HyPhy

The goal of this practical is to get you started on HyPhy. There are so many more analyses that you can do with this program than could be possibly explored in one session, but this shall help break the ice.



Instructions


1. Install

  • Make a folder for this practical.
  • Download the latest version of HyPhy for your appropriate OS here. (Since HyPhy is developed on a Mac, the MacOSX version might be slightly more up to date than the Windows version).
  • Unzip both packages into the practical folder.
  • Read the "README" file in the HyPhy folder to roughly find your way around.


2. Work through the tutorial in "Getting Started With HyPhy.pdf"

  • You will need to keep this pdf open in a parallel window for quick reference
  • Skimm the first 3 pages to get a quick overview over the power of HyPhy.
  • When you start HyPhy for the first time, just press OK to the start up screen, you do not need to choose something there. You can open all these options from within HyPhy too.
  • Work through the "Example: Basic Analysis" (page 4-11) using an alignment of the p51-subunit of the reverse transcriptase gene of HIV-1 sample data set (this is provided with the HyPhy installation in the file "p51.nex" in the folder "data").
  • If you have more time, work through further sections of the HyPhy tutorial or explore HyPhy by doing your own analyses.



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