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The programs normally used for phylogenetic prediction are the PHYLIP programs or PAUP. For simple data sets, the tree may be calculated by hand as illustrated below.




1. The following distances are found among four sequences M, N, O, and P:

  1. Draw all possible unrooted trees for the four sequences M, N, O, and P by labeling the X's.
  2. Based on the most closely related sequences in the table, choose the most likely tree.
  3. Label the tree branches with lowercase letters m, n, o, p, and q (where the lowercase x is indicated), being the branch going to node M, etc.:
  4. Calculate the lengths of the tree branches using the Fitch–Margoliash method described in the class notes.
  5. Calculate the branch lengths and the position of the tree root using the UPGMA method as described in the class notes.
  6. What assumptions are made by the above methods regarding mutation rates in the different branches of the evolutionary tree?




 

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