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    Assign 5 - GR5 - S22324

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    Trần Vĩnh Bảo Ngọc

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    Assign 5 - GR5 - S22324

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    Trần Vĩnh Bảo Ngọc
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    ASSIGN 5_GR5_S22324

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    Assign 5 - GR5 - S22324

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    Trần Vĩnh Bảo Ngọc

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    of 6

    VIETNAM NATIONAL UNIVERSITY

    INTERNATIONAL UNIVERSITY – SCHOOL OF BIOTECHNOLOGY

    BIOINFORMATICS

    Instructor: Nguyễn Minh Thành

    Date of submission: 13/5/2024

    ASSIGNMENT 5: PHYLOGENY

    Group 5 _ Group members:

    Seq. Full name Student ID % contribution (total = 100%)

    1
    Nguyễn Thị Lâm Anh BTBTIU21037 25

    2 Đinh Ngọc Vân Châu BTBTIU21042 25

    3 Nguyễn Ngọc Bảo Hân BTBTIU21164 25

    4 Trần Vĩnh Bảo Ngọc BTBTWE21113 25

    Total score: /100


    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)

    Figure 1. Result of Amino Acid Composition

    a. Ala of Pan troglodytes: 8.20%

    Ala of Macropus robustus: 8.23%

    b. Met of Homo sapiens: 1.41%

    Met of Mus musculus: 1.01%

    c. Gly of Gorilla gorilla: 9.22%


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

    Figure 2. Result of pairwise distance computation


    a. Which species is the closest relative to human?
    The closest species relative to human is Pan troglodytes (Chimpanzee).The p-distance between
    Pan troglodytes and Human is 0.0201
    b. Which species is the most distant relative to human?
    The most distant species relative of human is Crocodylus johnsoni (Crocodile). The p-distance
    between Crocodylus johnsoni and Human is 0.1831
    c. How much does a distance between Kangaroo & Gorilla?

    There is no connection between these 2 species

    Questions 3: Show NJ tree with the branch lengths

    Figure 3. Neighbor-Joining Tree


    a. Calculate a distance between Chimpanzee & Gorilla = 0.04 + 0.01 + 0.05 = 0.1
    b. Calculate a distance between Human & Baboon = 0.04 + 0.01+ 0.04 + 0.11 = 0.2

    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)

    Fig 4. Neighbor-joining tree (NJ)

    Fig 5. Maximum likelihood tree (ML)


    => These two trees do not have the same topology. There are differences in the branching
    patterns of Macropus Robustus & Mus musculus and Rhinolophus pumilus groups. In the ML
    tree, Rhinolophus pumilus is separated from the group, while the NJ tree places all three in the
    same group.

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

    Fig 6. The sum of branch length (SBL) of Neighbor-Joining Tree (left) and Maximum likelihood
    tree (right)
    SBL of NJ: 1.21778294
    SBL of ML: 1.75287041

    c. Identify the clades that are well supported in both trees (the bootstrap value > 80% & list
    all species of the clade).
    - 100%: the clade of Pan troglodytes, Homo sapiens, Gorilla gorilla, Papio hamadryas in
    both ML and NL tree.
    - 81%: the clade : Pormacanthus imperator, Hyla japonica, Crocodylus johnsoni in NJ tree.
    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:


    - Informative positions: must have at least 2 different kinds of nucleotide (bases) on at least 2
    sequences.
    => The 2nd and 10th position has 2 bases and each base appeared twice.

    b. Create a pseudo sample with defined positions below:

    Seq. 1 1 2 2 10 7 7 1 10 1
    1 A A C C T C C A C A
    2 A A C G C C C A T A
    3 A A G G C C C A C A
    4 A A G C T C C A T A

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