Assignment 3

Assignment 3 - A B C D A - 1.2 0.9 1.7 B - 1.1 1.9 C - 1.6...

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Introduction to Bioinformatics/Elements of Bioinformatics Assignment 3 Due: April 21, 2009 Submit in class or via email to bcwwong@hku.hk 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:
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Unformatted text preview: A B C D A - 1.2 0.9 1.7 B - 1.1 1.9 C - 1.6 D - Construct a rooted tree showing the relationships between A, B, C, and D by UPGMA. (10%) 5. Consider the following alignment and four possible trees from these sequences: Wombat GTTAATGAGTGGTTATCCAGAAGTGAGATA Opossum GTTAATGAGTGGTTATTCAGAAGTGAGATA Rhinoceros GTTAATGAGTGGTTTTCCAGAAGTGAAATA Pig GTTAATGAGTGGTTTTCTAGAAGCGAAATA Hedgehog GTGAATGAATGGCTTTCCAGAAGTGAACTG Human GTTAATGAGTGGTTTTCCAGAAGTGAACTG Hare GTTAACGAGTGGTTCTCCAGAAGTGAAATG Which of the following is correct according to the parsimony criterion? A: Tree 1 is preferable to all other trees. B: Trees 1 and 2 are preferable to Trees 3 and 4. C: Trees 1 and 3 are preferable to Trees 2 and 4. D: Trees 1 and 4 are preferable to Trees 2 and 3. Explain your answer. (7%) -- END --...
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This note was uploaded on 07/29/2010 for the course BIOC BIOC1805 taught by Professor Dr.brianwong during the Summer '09 term at HKU.

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Assignment 3 - A B C D A - 1.2 0.9 1.7 B - 1.1 1.9 C - 1.6...

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