Phylogeny Homework
October 28, 2008
Homework Assignment Number 6
For this homework assignment take between 10 and 15 protein sequences which are at least 30% identical or better and:
1) make a multiple sequence alignment with them using ClustalW and2) make two phylogenies, one using UPGMA method and the other using the Neighbor Joining method
Describe the resulting alignments and include the phylogenies in a message to homework218@cmgm.stanford.edu. Mention if the trees seem reasonable biologically or taxonomically by comparison with standard taxonomies (NCBI Taxonomy Page). Do the two trees have the same topology? Do the trees have the same branch lengths? If the two trees are not the same, describe the differences and indicate why you think the two methods differ. Are the differences significant?
The best way to find 10-15 protein sequences which are 30% identical or better is to look at the results of your previous homework in which you performed a database search. Go down the list of similar proteins to either the top 10 sequences or those with > 30% identity and use those sequences to make your alignment. If you have less than 10 such sequences, then choose another sequence for this study.
This assignment is due on November 4, 2008 sent to homework218@cmgm.stanford.edu.
If you have not yet decided on a project to do for the class, please send an email with your ideas directly to me, brutlag@stanford.edu.