Lecture 6

The movie of the Ranoids lecture is posted.

The assignment for this lecture is to aligh the sequences in this file: Align This!

(The file is already in NBRF format, and ready to read into ClustalX

1. Download Clustal X from ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/

2. Download literature in pdf format:

ClustalX manual

ClustalX published paper

ClustalX Tips paper

3. Align the sequences (as we discussed in class) using ClustalX.

4. Fine-tune the alignment by hand using MacClade or some other sequence alignment program.

5. Analyze the sequences using PAUP, including bootstrap or jackknife analyses. Make some decisions about:

a. Which character regions to exclude, if any

b. Whether to analyze several different alignments

c. Whether to use indels as distinct characters (or not), how to weight them, etc.

6. Turn in the following by email:

a. Your alignment(s) as a nexus file.

b. A MS Word, Text, or pdf file with the results of your analyses.

c. A few paragraphs (Word or text file) explaining what you did (for 5a, b, and c) and why you did it. Write this in the style of a Materials and Methods section of a paper.