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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.

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

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  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.

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

  7. Identify orthologous and paralogous relationships

  8. 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?

  9. NJ

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

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

  12. MP

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