Assignment 8:
Tree Assignment
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UPGMA |
Neighbor joining |
Unweighted |
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Jukes Cantor |
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Kimura |
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For example, what is the difference in the distance matrix and does this affect the trees you see?Which gives the most appropriate tree do you believe and why?
Uncorrected distance is an algorithm that calculates the observed distances between the sequences with no correction for multiple substitutions. This is used for both nucleic acids or protein sequences.
The Jukes-Cantor method is a technique that indicates that the nucleotide subsitution rate is the same for all nucleotides (A,C,G,T). This technique assumes an equality of substitutions rates among the various sites and frequency of the nucleotides. This model shows the maximum likelihood estimate of the number of nucleotide substitutions between sequences.
Kimura is a distance formula that is good at approximating PAM distances by measuring the fraction of amino acids that are different between the sequences and calculating their respective distances.
Discuss the two different branch methods for tree building- UPGMA and Neighbor joining.What are their differences?Similarities?
UPGMA (Unweighted Pair Group Method with Arithmetic mean) is a technique used to create trees. They assume that there is a constant rate of evolution. This method is used commonly in producing guide trees for more enhanced projects. This produces a rooted tree.
Neighbor Joining is another method for creating trees. This technique uses the DNA or protein sequence data. The program needs the distance between each type of taxa. This does not assume that all lineages evolve at the same rate. It produces an unrooted tree.
How are both methods different from Maximum Parsimony?
Maximum Parsimony is a statistical method used to estimate phylogenies. This technique uses a matrix with phylogenetic characters for each phylogenetic tree for a taxa. It minimizes the total number of evolutionary steps required to explain a set of data. This ultimately shortens the tree length.
What is Maximum Likelihood?
Maximum Likelihood is an optimality criterion used to determine the best way to fit a mathematical model to a given set of data. Maximum likelihood picks the values of model parameters that make the data more likely than other parameters would determine. this usually gives a unique solution.
Finally, do your trees make biological sense to you?Are the most distantly related species the farthest apart?
The trees do not make much sense. The human and frog seem to be related in the trees made. This might be due to incorrect search parameters or poor trimming of the various sequences.
Protein Trees:
Use Seqweb to make protein trees with your translated proteins.
Protein Tree |
Settings |
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Select two or three different levels of BLOSUM or PAM.How does this affect the trees?
Changing the levels of BLOSUM caused the branches to be moved in different places which causes the relationship between all the organisms to change.
Compare the trees you got with Nucleic Acids and with proteins.Which tree (protein or nucleic acid) do you feel is appropriate for your gene of interest and why?
I believe the protein is better for the gene of interest because it shows the best relationship between all of the organisms.
Finally, do your trees make biological sense to you?Are the most distantly related species the farthest apart?
Yes, they do make biological sense. The ones that are not directly related are farther apart and the ones that are similar are closer to another.