CPSC 485 Computational Bioinformatics
Homework #4, Due 05/06/09
Problem 1-3. Assume the following is the distance matrix of 9 genes. Cluster the 9 genes
using the algorithms we discussed in classes.
g1 g2 g3 g4 g5 g6 g7 g8 g9
g1 0 38 58 13 15 27 10 19 12
g2 38 0 86 49 67 60 25 43 89
g3 58 86 0 83 37 66 78 95 11
g4 13 49 83 0 67 31 45 82 36
g5 15 67 37 67 0 5 94 2 51
g6 27 60 66 31 5 0 96 28 88
g7 10 25 78 45 94 96 0 85 43
g8 19 43 95 82 2 28 85 0 67
g9 12 89 11 36 51 88 43 67 0
Problem 1. Cluster the genes using the HIERARCHICALCLUSTERING algorithm on page
345. The distance between two clusters is calculated as the average distance between
their elements.
Problem 2. Cluster the genes using the CAST algorithm on page 354. The distance
threshold is set to
θ
= 33.
Problem 3. Cluster the genes using the UPGMA algorithm on page 366.
Problem 4. Assume the following is the distance matrix of 6 leaves in a tree. Reconstruct
the tree using the ADDITIVEPHYLOGENY algorithm on page 364.
A B C D E F
A 0 4 7 10 12 11
B 4 0 7 10 12 11
C 7 7 0 9 11 10
D 10 10 9 0 10 9
E 12 12 11 10 0 9
F 11 11 10 9 9 0
