Today in MEGA: Sequence Data Explorer Constructing Phylogenetic Trees

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Presentation transcript:

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