1. Download the ZP3 nucleotide alignment from the course website. Open the sequences in Se-Al and check the alignment by eye and make any corrections needed. Export sequence as Nexus format.

2. Open the alignment in PAUP* and execute the file. Select parsimony as the optimality criterion. Generate a maximum parsimony tree using a variety of search modes (exhaustive, heuristic, branch and bound). Do you always get the same tree? What is the tree length of the most parsimonious tree? What is the length of the next closest tree, and how do they differ? Perform a bootstrap analysis and indicate which branches have strong support.

3. Generate a neighbor-joining tree using PAUP*. Save the tree to a file. Perform a bootstrap analysis to determine which branches have high support.

4. In order to perform a likelihood analysis, we need to choose a model of evolution. In order to do this, we will check which model best fits the data. Check the likelihood of the data given the NJ tree generated in step 3 for a variety of models.
a. Load the tree into PAUP* as a constraint (under analysis, load constraint).
b. Select Analysis type as likelihood. Select Analysis then Likelihood settings. Change the settings to represent the Jukes Cantor model (see back for models), then calculate the likelihood. Select optimality criterion as likelihood. Perform analysis with enforcing topological constraint. What is the likelihood? Get a screen shot using thr grab program showing this result and put it in your report.
c. Do the same as in b, but change the settings to represent the HKY model. What is the likelihood under this mode?
d. Perform a likelihood ratio test to choose between the HKY and JC models. Which did you choose and why?

5. Now perform a modeltest analysis to choose a model automatically:
The input of Modeltest is a set of likelihood scores corresponding to the specific data set and each one of 56 models. The easiest way of obtaining these scores from an alignment of DNA sequences is using PAUP*. A block of commands for PAUP* is provided below in the file "modelblockPAUPb10”. Follow these steps:
      1.       Open your data file and execute it in PAUP
      2.       Open the command file ("modelblockPAUPb10) and execute it
      3.       PAUP* starts to work in the data following the commands. Once is finished you will see a file called "model.scores" in the same directory as the command file. Run the file "model.scores" through Modeltest. This is done in a Macintosh just double-clicking in the application provided.

6. Perform a likelihood analysis using the model you selected. Paste the paupblock from model test output into the nexus file and reopen it in PAUP. This will automatically set the models for likelihood analysis. Does the tree correspond to the parsimony and NK tree generated previously? Perform a bootstrap analysis. Which branches have high support?

Write up a short report of the lab answering the questions above. Please also indicate any problems you had with the lab.