Introduction to Bioinformatics/Elements of Bioinformatics
Assignment 3
Due: April 21, 2009
Submit in class or via email to [email protected]
1a
Write the following phylogenetic tree in the Newick tree format. (3%)
1b.
Find the root of the above tree by the mid-point rooting technique. Write the resulting
rooted tree in the Newick tree format. (2%)
2.
Consider the following alignment:
Seq1.
CTAAGGCTTACGATTACGAGGATCCAAATGGCACCAATGCT
Seq2.
CTA-CGCTTACGACAACGAGGATCCGAATGGCACCATTGCT
Calculate the Juke-Cantor distance between the 2 sequences. (2%)

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3.
Consider the following trees:
a)
Which of them are the same, as rooted additive trees? (1%)
b)
Which of them are the same, as unrooted additive trees? (1%)
c)
Which of them are the same, as rooted topological trees? (1%)
d)
Which of them are the same, as unrooted topological trees? (1%)
4.
A distance matrix is constructed from the multiple alignment of 4 sequences: