Answered: Special note: Use the tree, observed…

Database System Concepts

7th Edition

ISBN:9780078022159

Author:Abraham Silberschatz Professor, Henry F. Korth, S. Sudarshan

Publisher:Abraham Silberschatz Professor, Henry F. Korth, S. Sudarshan

Chapter1: Introduction

Section: Chapter Questions

Problem 1PE

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Question

This is the 3rd time I am asking this question on this platform. Previous answers were wrong or incomplete.
Please, do not give me the same old wrong answers. Write a workable code to solve this problem and I will upvote

Special note: Use the tree, observed states at the leaves, branch lengths and the JC69,
calculate the posterior probability of [A,G,C,T] at node 15. Build on the code already provided.

# Use this character state vector indicating
# the nucleotide at leaf nodes 1-8
site1=["A","C","C","C","G","C","C","A"]

# Use this tree structure
tree4 = {
15: ['N',{"node": 14, "branch": 0.02}, {"node": 8, "branch": 1.1}],
14: ['N',{"node": 13, "branch": 0.11}, {"node": 7, "branch": 1.2}],
13: ['N',{"node": 12, "branch": 0.12}, {"node": 6, "branch": 0.8}],
12: ['N',{"node": 11, "branch": 0.64}, {"node": 9, "branch": 0.11}],
11: ['N',{"node": 3, "branch": 0.26}, {"node": 10, "branch": 0.24}],
10: ['N',{"node": 4, "branch": 0.02}, {"node": 5, "branch": 0.08}],
9: ['N',{"node": 1, "branch": 0.4}, {"node": 2, "branch": 0.6}]
}
for i in range(1, 9):
tree4[i] = ['L']

# JC69 model to generate Q matrix
def JC69():
Q = np.full((4,4),0.25)
np.fill_diagonal(Q,-.75)
Q = Q/0.75
return Q

# Initialize rate matrix
Q = JC69()

# Answer

Use the tree, observed states at the leaves, branch lengths and the JC69, calculate the posterior probability of [A,G,C,T] at node 15.
A
с
G
C
1
3
5
7
9
с
2
(12)
(11)
C
4
(10)
(13)
(14)
с
6
15
A
8

# Use this character state vector indicating
# the nucleotide at leaf nodes 1-8
sitel=["A","c","c","c","G","C","C","A"]
# Use this tree structure
tree4 {
"branch": 1.1}],
15: ['N', { "node": 14, "branch": 0.02}, {"node" : 8,
14: ['N', { "node": 13, "branch": 0.11}, {"node": 7, "branch": 1.2}],
13: ['N',{"node": 12, "branch": 0.12}, {"node": 6, "branch": 0.8}],
12: ['N',{"node": 11, "branch": 0.64}, {"node": 9, "branch": 0.11}],
11: ['N', { "node": 3, "branch": 0.26}, {"node": 10, "branch": 0.24}],
10: ['N', { "node": 4, "branch": 0.02}, {"node": 5, "branch": 0.08}],
9: ['N',{"node": 1, "branch": 0.4}, {"node": 2, "branch": 0.6}]
}
for i in range(1, 9):
tree4[i] = ['L']
#JC69 model to generate Q matrix
def JC69():
np. full ((4,4), 0.25)
np. fill_diagonal (0,-.75)
Q
Q/0.75
return Q
#Initialize rate matrix
JC69 ( )
# Answer

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