1. Today in MEGA:
Sequence Data Explorer
Constructing Phylogenetic Trees
Tree Explorer
Branch & Bound Search

2. Start MEGA (File -> Open Data) or
Open (double click) the file ldh_a-c.meg with the multiple alignment we created last week

3. Sequence Data Explorer
Highlight different types of sites (conserved, variable, informative, singleton, 0-fold…)
Translate the DNA sequence to protein and back to DNA

4. Neighbor-Joining Tree
Select Phylogeny -> Construct Phylogeny -> Neighbor-Joining command to display the analysis preferences dialog box.

5. Neighbor-Joining Tree
Select Phylogeny -> Construct Phylogeny -> Neighbor-Joining command to display the analysis preferences dialog box.
In the Options Summary tab, click Model pull-down and select Nucleotide Kimura 2-parameters option.
Click Compute to accept the defaults for the rest of the options.

7. Tree Explorer: Place the root on a branch Flip sub-tree Swap sub-tree
Compress/Expand sub-tree

8. Identify orthologous and paralogous relationships

9. The file flu.fas contains the sequences of PA protein from
Current “swine flu” (marked with SF)
Human H1N1
Avian H1N1
Swine H1N1
Use Mega to align the sequences, and construct Neighbor-Joining and Maximum-Parsimony trees.
For the MP method, use branch & bound.
Are the first MP tree and the NJ tree congruent?
Is “swine flu” a good descriptor in the case of the PA gene? Hint: Is “swine flue” a clade?

10. NJ

11. MP (out of 315 when using equally parsimonious trees)

12. MP: Place a root in the same place in both trees.

13. MP