Potential project ideas:

1. I am interested in origin of domesticated dogs, do a phylogeny to determine closest wild relative.

2. I know Neanderthal has been sequences, so I will compare some Neanderthal, human and chimpanzee sequences. How are they similar and different? Can you find any potential pyrosequencing errors?

3. I am interested in the evolution of the SRY gene, has it been subject to positive selection?

4. The morpheaus gene was analyzed by dN/dS counting methods, can I learn anything by re-analyzing the data with maximum likelihood and adding more species?

5. Analyze gene duplication in humans compared to chimpanzee.

6. A recent news report indicated the presence of a dangerous HIV strain recently found in Seattle. I will investigate HIV diversity.

7. How similar are the different flu strains, in particular avain and human influenza?

8. What is the sabertooth tiger's position in a felid phylogeny?

9. How does dS correlate with level of gene expression?

10. Reproductive protein evolve rapidly, is there any correlation with mating system classification?

11. Investigate the use of comparative sequencing data for assigning functional portions of the genome (e.g. Encode project).