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Group-21 - Bioinformatic - Assignment-5 - Phylogeny - Fix

This document contains the assignment submission of group 21 for their bioinformatics phylogeny assignment. It reports the frequency of various amino acids in different species, identifies chimpanzees as the closest and crocodiles as the most distant relative of humans based on pairwise distances. It also analyzes the neighbor joining and maximum likelihood phylogenetic trees constructed, noting two groups with over 50% bootstrap support that are consistent between the trees.

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416 views6 pages

Group-21 - Bioinformatic - Assignment-5 - Phylogeny - Fix

This document contains the assignment submission of group 21 for their bioinformatics phylogeny assignment. It reports the frequency of various amino acids in different species, identifies chimpanzees as the closest and crocodiles as the most distant relative of humans based on pairwise distances. It also analyzes the neighbor joining and maximum likelihood phylogenetic trees constructed, noting two groups with over 50% bootstrap support that are consistent between the trees.

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Huỳnh Như
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© © All Rights Reserved
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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)

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