Table of Contents

Tutorial 5 - UPGMA, Neighbor Joining

Problem 1 - UPGMA

Using UPGMA reconstruct the phylogenetic three that is consistent with the given data.
Assume a set of sequences A = {a, b, c, d, e} and the corresponding distance matrix D.

How can you compute the distance matrix D?
D a b c d e
a 0
b 12 0
c 12 4 0
d 12 6 6 0
e 12 6 6 2 0
  1. Check the assumption for UPGMA
  2. Reconstruct the phylogenetic tree using UPGMA

Problem 2 - NJ

Using NJ reconstruct the phylogenetic three that is consistent with the given data.
In this case, assume a set of sequences A = {a, b, c, d} and the corresponding distance matrix D.

D a b c d
a 0
b 4 0
c 10 8 0
d 9 7 9 0

Similarly to the previous problem:

  1. Check the assumption for NJ
  2. Reconstruct the phylogenetic tree using NJ