How to create a phylogenetic tree

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In this section of class, we'll go through the process of generating a phylogenetic tree from sequence data. This process can be broken up in subsections a variety of ways, but one way to do it is this:

  1. Decide what sequences to use in the analysis
  2. Obtain the required sequence data experimentally or from databases
  3. Assemble these sequences in a multiple sequence alignment (= identify homologous residues)
  4. Use this alignment to generate phylogenetic trees
  5. Interpret the resulting tree

After going through this process in detail, we'll follow it up with a real-life example analysis.