Download as DOCX, PDF, TXT or read online from Scribd
Download as docx, pdf, or txt
You are on page 1/ 2
BT337IU Bioinformatics
Assignment 5
Phylogeny
Due date: 13:00 Fri. 21 Nov. 2024
(Submission via email: Bioinfosiu@gmail.com)
In this assignment, you will use sequences of mitochondrial cox1 gene (for cytochrome c oxidase subunit 1) to infer the phylogenetic relationships among 12 species of terrestrial vertebrates from different major lineages: human, chimp, gorilla, baboon, lemur, bat, mouse, kangaroo, platypus, croc, frog and angelfish. Mitochondrial genes are commonly used in molecular phylogenetic studies due to their high substitution rates and the lack of recombination relative to nuclear genes.
Sequence alignment
1. Select the “vertebrate_cox1.fas” file.
2. Perform ClustalW alignment. 3. Once the alignment is complete, save the current alignment session with the name “vertebrate_cox1.mas”. This will allow the current alignment session to be restored for all tasks below.
Calculate the amino acid composition
4. Perform Sequence translation to calculate the amino acid composition.
Compute the Proportion of Amino Acid Differences
5. Perform Pairwise Distances for amino acids & select the p-distance under Model/Method.
Build phylogenetic trees
6. Select Phylogeny | Construct/Test Neighbor-Joining Tree menu option. In the Analysis
Preferences window: (i) select the p-distance model option from the Model/Method drop- down menu, (ii) select Nucleotide option from the Substitutions Type drop-down menu, (iii) and Bootstrap method for the Test of Phylogeny option. Input 500 for the No. of Bootstrap Replications. Save/Print the original tree to a PDF file. 7. Select Phylogeny /Test Maximum Likelihood Tree menu option. In the Analysis Preferences window: (i) select the Tamura-Nei model option from the Model/Method drop-down menu, (ii) select Nucleotide option from the Substitutions Type drop-down menu, (iii) and Bootstrap
1 method for the Test of Phylogeny option. Input 100 for the No. of Bootstrap Replications. Save/Print the original tree to a PDF file.
Question 1: Report frequency (%) of the following amino acids:
a. Ala of Pan troglodytes (Chimpanzee) & Macropus robustus (Kangaroo)
b. Met of Homo sapiens (Human) & Mus musculus (Mouse) c. Gly of Gorilla gorilla (Gorilla)
Questions 2: Based on the pairwise distances for amino acids, report:
a. Which species is the closest relative to human? b. Which species is the most distant relative to human? c. How much does a distance between Kangaroo & Gorilla?
Questions 3: Show NJ tree with the branch lengths
a. Calculate a distance between Chimpanzee & Gorilla
b. Calculate a distance between Human & Baboon
Questions 4: Compare the NJ and ML trees:
a. Do two trees have the same topology? (show ML tree in order to compare with NJ tree) b. Report the sum of branch length for each tree. c. Identify the clades that are well supported in both trees (the bootstrap value > 80% & list all species of the clade). Questions 5: The table below show the alignment of 4 sequences with the length of 10 bp.
Seq. 1 2 3 4 5 6 7 8 9 10 1 A G T A G T C T G C 2 A G T C G A C A G C 3 A C T C G G C T C T 4 A C T C T C C T G T
a. Identify the informative positions
b. Create a pseudosample with defined positions below:
