Description
QUESTION 1
What set of relationships are now shown?
1.5 points
QUESTION 2
What is the Newick format of the correct tree?
((((Bbelcheri,Hsapiens),Aplanci)),(((Hvulgaris,Myessoensis),(Dgigantea,Nvectensis))));
(((((Bbelcheri,Hsapiens),Aplanci),Myessoensis)),(((Hvulgaris,Nvectensis),Dgigantea)));
(((((Bbelcheri,Hsapiens),Aplanci),Myessoensis)),((Hvulgaris,(Dgigantea,Nvectensis))));
(((((Bbelcheri,Myessoensis),Hsapiens),Aplanci)),((Hvulgaris,(Dgigantea,Nvectensis))));
1.5 points
QUESTION 3
What is the log likelihood of the optimal tree that IQ-TREE found?
1.5 points
QUESTION 4
Which amino-acid exchange rate model was did we use?
1.5 points
QUESTION 5
Which amino acid frequencies did we use to estimate the tree?
1.5 points
QUESTION 6
Which rate heterogeneity did we use to estimate the tree?
1.5 points
QUESTION 7
What is the least frequent amino acid in the alignment?
1.5 points
QUESTION 8
What is the most frequent amino acid in the alignment?
1.5 points
QUESTION 9
Based on our discussion of unroooted trees, and your visualization of the unrooted tree, what is the oldest divergence event on the unrooted tree?
1.5 points
QUESTION 10
Compare the cladogram and phylogram. What has changed in the cladogram, compared to the phylogram?
1.5 points
QUESTION 11
Carefully examine the midpoint rooted tree. What is the oldest divergence event on the midpoint rooted tree?
1.5 points
QUESTION 12
How many genes are included in the clade that includes the common ancestor and all the descendents of any gene labelled in the phylogeny as “barHlike” or “BarHlike”? (The hyphen has been removed; other places this is: BarH-Like).
1.5 points
QUESTION 13
Compare the **species** phylogeny you made to the gene phylogeny. In particular, examine the area of the phylogeny around the *Nematostella* Hox-C5 gene. Are the species relationships reflected in the gene tree?
1 points
QUESTION 14
Locate the Hox-C5 gene in humans and the Hox-C5 gene in Nematostella. What does the tree tell you about the relationship between these gene copies?
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Paul
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Paul 2023-09-01 11:59:51 2023-09-01 11:59:51 Bioinformatics Worksheet