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TOPIC:
UPGMA
• Distance-based methods –
• Character-based methods –
Examples : Parsimony ,
Maximum Likelihood
UPGMA
UPGMA : Unweighted Pair Group Method with Arithmetic Mean
Developed by Sokal and Michener in 1958.
It is a Sequential clustering method
Type of distance based method for Phylogenetic Tree construction
UPGMA is the simplest method for constructing trees.
Generates rooted trees
Generates ultra metric trees from a distance matrix
Uses a simplest algorithm
Input: Distance matrix containing pairwise statistical estimation of
aligned sequences
• The algorithm constructs a rooted tree that reflects the structure present in a
pairwise similarity matrix.
• At each step, the nearest two clusters are combined into a higher-level
cluster.
𝐷 Dik +𝐷 𝑗𝑘
𝑖𝑗 , 𝑘 = 2
Delete columns and rows corresponding to i and j and add one for (ij). If there are
two or more groups left, go back to the first step
Computational tools
• MEGA
• PHYLIP
• MVSP
• MVSP87
• SAS
• SYN-TAX
• NTSYS
• DendroUPGMA
Advantages
simple algorithm
Fastest method
easy to compute by hand or a variety of software
Trees reflect phenotypic similarities by phylogenetic distances
Data can be arranged in random order prior to analysis
Rooted trees are generated that are easy to analyze
Disadvantages
A B C D E F
A 0 1 3 6 7 10
B 1 0 3 6 7 10
C 3 3 0 5 6 9
D 6 6 5 0 1 7
E 7 7 6 1 0 8
F 10 10 9 7 8 0
2. Group the 2 most closely related sequences
A B C D E F
A 0 1 3 6 7 10 0.5
A
B 1 0 3 6 7 10
0.5
C 3 3 0 5 6 9 B
D 6 6 5 0 1 7
E 7 7 6 1 0 8
F 10 10 9 7 8 0
3. Recalculate the distance matrix and take the next
smallest distance
A/B C D E F
A/B 0 3 6 7 10 0.5
A
C 3 0 5 6 9
0.5 B
D 6 5 0 1 7
E 7 6 1 0 8 0.5
D
F 10 9 7 8 0
0.5 E
3. Recalculate the distance matrix and take the next
smallest distance
A/B C D/E F
0.5
A/B 0 3 6.5 10 A
1
C 3 0 5.5 9 0.5 B
0.5
D
0.5 E
3. Recalculate the distance matrix and take the next
smallest distance
A/B/C D/E F
0.5
A/B/C 0 6 9.5 A
1
0.5
D
2.5
0.5 E
3. Recalculate the distance matrix and take the next
smallest distance
A/B/C/D/E F 0.5
A
A/B/C/D/E 0 8.5 1
0.5
1.5 B
F 8.5 0
1.5
C
1.25
0.5
D
2.5
0.5
E
4.25
F