Today in MEGA: Sequence Data Explorer Constructing Phylogenetic Trees Tree Explorer

Today in MEGA:

• Sequence Data Explorer

• Constructing Phylogenetic Trees

• Tree Explorer

• Branch & Bound Search

• Start MEGA (File -> Open Data) or

• Open (double click) the file ldh_a-c.meg with the multiple alignment we created last week

Sequence Data Explorer• Highlight different types of sites (conserved, variable, informative, singleton, 0-fold…)

• Translate the DNA sequence to protein and back to DNA

Neighbor-Joining Tree

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

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.

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

Identify orthologous and paralogous relationships

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?

NJ

MP (out of 315 when using equally parsimonious trees)

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

MP