This web page was produced as an assignment for Genetics 564, an undergraduate course at UW-Madison. http://genetics564.weebly.com/
Protein Phylogeny
What is phylogeny?
Phylogeny is the evolutionary history of a species or group. Phylogeny is visually displayed in a tree formation. How the branches of the tree are connected demonstrate the relationships among the organisms. The closer the node is between two organisms, the closer they are related. The nodes on the tree represent a common ancestor between each specie. All species are at the end of the branches and the node that is connected to all the organisms is the common ancestor for the entire tree. Phylogeny allows you to visualize how species are related to one another.
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PTPN2 ClustalW Omega
In order to create phylogenetic trees for PTPN2 I first had to use ClustalWOmega. This program allows you to insert your FASTA sequences for each organism and it will align them in order to compare and contrast species. The program then is able to use the aligned sequences to make phylogenetic trees (average distance joining and neighbor joining) like the ones below.
Phylogenetic Trees
% Identity Method
The % Identity method compares sequences based of their percent relatedness in order to deduce similarity (1).
BLOSSUM Matrix Method
The BLOSSUM Matrix method finds similarity between sequences with the use of a scoring system. TThe score are based off of wheter the two amino acids match and the likelihood of another match occurring by chance. The two scores are added together and then assigned each aligned pair of amino acids (1).
Average Distance Joining Method
The Average Distance method utilizes similarity scores to determine which species are most closely related. This method works off of the assumption that both species diverged equally from the common ancestor (1).
Neighbor Joining Method
The Neighbor Joining Method utilizes similarity scores to see which species are most closely related. The branch lengths in Neighbor Joining are calculated based off of the amount of change after the species diverged (1).
Average Distance Using BLOSUM62
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Neighbor Joining Using BLOSUM62
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References
- http://genetics564.weebly.com/homology--phylogeny.html
- [ClustalOmega] http://www.ebi.ac.uk/Tools/msa/clustalo/