VIETNAM NATIONAL UNIVERSITY

HO CHI MINH INTERNATIONAL UNIVERSITY

BIOINFORMATICS
ASSIGNMENT 5
PHYLOGENY

GROUP 21:
1. Võ Huỳnh Như - BTBTIU18367
2. Cao Sang - BTBTIU18324
3. Lê Thục Đoan Trinh - BTBTIU18254
4. Nguyễn Uyên Y Xuân - BTBTIU18301

Date of submission: November 27, 2020

Question 1: Report frequency (%) of the following amino acids:

a. Ala of Pan troglodytes (Chimpanzee) & Macropus robustus (Kangaroo)

_ Ala of Pan troglodytes (Chimpanzee): 8.2 %
_ Ala of Macropus robustus (Kangaroo): 8.233 %
b. Met of Homo sapiens (Human) & Mus musculus (Mouse)
_Met of Homo sapiens (Human): 1.406 %
_ Met of Mus musculus (Mouse): 1.006 %
c. Gly of Gorilla gorilla (Gorilla)
_ Gly of Gorilla gorilla (Gorilla): 9.218 %

Questions 2: Based on the pairwise distances for amino acids, report:

a. Which species is the closest relative of human?
_ Chimpanzee (Pan troglodytes) are the closest relative of human
b. Which species is the most distant relative of human?
_ Crodile (Crocodylus johnsoni ) are the most distant relative of human

Questions 3: Which groups in the NJ tree have Bootstrap support value

>50%?

NJ tree
 There are 2 groups in the NJ tree have Bootstrap support value >50%.
Group 1: Pan troglodytes (Chimpaneze), Homo sapiens (Human), Gorilla
gorilla (Gorilla) and Papio hamadryas (Baboon)
Group 2: Crocodylus johnsoni (Crocodile), Hyla japonica (Frog) and
Pomacanthus imperator (Angelfish)
Questions 4: Compare the NJ and ML trees:
a. Do two trees have the same topology? Show NJ & ML trees
_ Two trees have the different topology.

NJ trees
 ML trees

b. Report the sum of branch length for each tree.

_ The sum of branch length of NJ tree = 1.21778294
_ The sum of branch length of ML tree = 1.74743661
c. Identify two groups that are well supported in all of two trees.
Two groups that are well supported in all of two trees:
_Group 1: Pan troglodytes (Chimpaneze), Homo sapiens (Human), Gorilla
gorilla (Gorilla) and Papio hamadryas (Baboon)
_Group 2: Crocodylus johnsoni (Crocodile), Hyla japonica (Frog) and
Pomacanthus imperator (Angelfish)