BIOINFORMATICS

PROF. M. MICHAEL GROMIHA

DEPARTMENT OF BIOTECHNOLOGY
INDIAN INSTITUTE OF TECHNOLOGY MADRAS

LECTURE - 10B
PHYLOGENETIC TREES II

Methods to construct phylogenetic trees

UPGMA method: unweighted pair group with arithmetic mean

Example

Consider five species (sequences), A, B, C, D and E. We compute the distance matrix as

follows.
D and E are closest to each other, so we combine these two and modify the matrix as
shown, taking the average of D and E (12 and 15) and replacing D and E rows with DE
row. The distances are recomputed for the new row using the given formula.

The procedure is repeated until we obtain the following.

Estimation of branch length

This is to estimate how much time it takes to diverge. the distance is divided equally
between the two terminal nodes.
The procedure is repeated for the common ancestor nodes until we the reach the root.
Neighbor’s relation method

Four point condition is applied in this method.

Neighbor joining method
Maximum likelihood method
Phylip
Input for Phylip is sequence alignment from MAFFT.
Select the output format for MAFFT according to the version of Phylip you are using.
How to run Phylip
Bootstrapping is done to check that the possibility of getting the same tree for
randomized sequences is extremely low, i.e. the tree constructed for our sequences is
unique and cannot be replicated by randomization of our sequences.
The proml program is used to get the tree by maximum likelihood method.
The outtree file can be viewed using TreeView.

The consensus tree can be obtained using consense.

To get the rectangular cladogram, use the option from the Tree menu.