VIETNAM NATIONAL UNIVERSITY

HO CHI MINH INTERNATIONAL UNIVERSITY

Group’s member: Đinh Lưu Nhật Quỳnh – BTBTIU18422

Huỳnh Ngọc Phương Như - BTBTIU18432

Trương Anh Thư – BTBTIU19121

Tôn Ngọc Minh Trang - BTBTIU18364

Course: Bioinformatics

Lecturer: Dr. Nguyen Minh Thanh

Question 1: Report frequency (%) of the following amino acids:
a. Ala of Pan troglodytes (Chimpanzee) & Macropus robustus (Kangaroo)
- Ala of Pan troglodytes (Chimpanzee): 8.20%
- Ala of Macropus robustus (Kangaroo): 8.23%

b. Met of Homo sapiens (Human) & Mus musculus (Mouse)

- Met of Homo sapiens (Human): 1.41%
- Met of Mus musculus (Mouse) : 1.01%

c. Gly of Gorilla gorilla (Gorilla)

- Gly of Gorilla gorilla (Gorilla): 9.22%

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

a. Which species is the closest relative of human?
b. Which species is the most distant relative of human?

Most distant

Closest
 a. Which species is the closest relative of human?
According to the p-distance, the p-distance between chimpanzee and human is the smallest one,
which is 0.0203. Thus, the closest relative of human is chimpanzee.
b. Which species is the most distant relative of human?
The p-distance between crodile and human which has the largest p-distance, which is 0.2022,
compared to p-distance of human and other species. This states out that the crodile and human
have the most distant relation.

Question 3: Which groups in the NJ tree have Bootstrap support value >50%?
Bootstrap support value indicates how many times out of 100 (in your case) the same branch was
observed
when repeating the phylogenetic reconstruction on a re-sampled set of your data.
- Bootstrap value > 95%: very high confidence
- Bootstrap value > 75%: high confidence
- Bootstrap value < 60%: low confidence
- Bootstrap value < 50%: very low or no confidence
Based on the NJ tree, the Bootstrap support values are mentioned on the nodes. Therefore,
groups that
have Bootstrap support value >50% are:
-Pan troglodytes | Chimpanzee and Homo sapiens | Human (96%)
- Pan troglodytes | Chimpanzee, Homo sapiens | Human and Gorilla gorilla | Gorilla (100%)
- Pan troglodytes | Chimpanzee, Homo sapiens | Human, Gorilla gorilla | Gorilla and Papio
hamadryas | Baboon (100%)
- Hyla japonica | Frog and Crocodylus johnsoni | Crodile (97%)
- Hyla japonica | Frog, Crocodylus johnsoni | Crodile and Pomacanthus imperator | Angelfish
(55%)
Questions 4:
Compare the NJ and ML trees:
a. Do two trees have the same topology? Show NJ & ML trees.
- Two trees have the same topology.

Pan troglodytes | Chimpanzee

0.04
0.01
96 Homo sapiens | Human
0.04
0.04
100
Gorilla gorilla | Gorilla
0.02 0.05
100
Papio hamadryas | Baboon
0.11
0.00
37
Ornithorhynchus anatinus | Platypus
0.11
0.00
42 Lemur catta | Lemur
0.00 0.10

Macropus robustus | Kangaroo

0.11

0.00
22
Mus musculus | Mouse
0.10
0.00
44 Rhinolophus pumilus | Bat
0.10

Pomacanthus imperator | Angelfish

0.12

0.01
79
Hyla japonica | Frog
0.12
0.00
54 Crocodylus johnsoni | Crodile
0.13

NJ tree
 Pan troglodytes | Chimpanzee
0.04

0.02
68
Homo sapiens | Human
0.05
0.06
100

Gorilla gorilla | Gorilla

0.05
0.07
100

Papio hamadryas | Baboon

0.03 0.13
34

Lemur catta | Lemur

0.05 0.12
44

Ornithorhynchus anatinus | Platypus

0.14
0.03
21

Macropus robustus | Kangaroo

0.14

0.03
0.06 14
52 Rhinolophus pumilus | Bat
0.10

0.10
59
Mus musculus | Mouse
0.11

1.22 Crocodylus johnsoni | Crodile

0.18

Pomacanthus imperator | Angelfish

0.05

Hyla japonica | Frog

1.68

MJ tree

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

- NJ tree: 1.21778294
- MJ tree: 1.74743648
c. Identify two groups that are well supported in all of two trees.
- Papio hamadryas | Baboon, Gorilla gorilla | Gorilla, Pan troglodytes | Chimpanzee, Homo
sapiens | Human.
- Crocodylus johnsoni | Crodile, Hyla japonica | Frog, Pomacanthus imperator | Angelfish