Introduction to Bioinformatics: CMSC54610-1, Spring quarter 2006.

Some frequently asked questions about the homework for Lecture 4

• When you say 'Try different PAM matrices' in ClustalW, did you mean for us to try different matrices (i.e. blusom, gonnet, etc.)? I'm not sure how I can use different PAM matrices as it seems that ClustalW uses only the PAM-350 matrix.
  • Yes, try Blosum and Gonnet. See the manual page on the website. You can also experiment with the gap penalties.
• Are the cladogram and a phylogram sufficient for tree outputs?
  • Yes, this is sufficient. See if you can get different tress by using different matrices.