Today in MEGA:

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• Today in MEGA
• Sequence Data Explorer
• Constructing Phylogenetic Trees
• Tree Explorer
• Branch Bound Search

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

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Sequence Data Explorer

• Highlight different types of sites (conserved,
  variable, informative, singleton, 0-fold)
• Translate the DNA sequence to protein and back
  to DNA

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Neighbor-Joining Tree

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

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Neighbor-Joining Tree

• Select Phylogeny -gt Construct Phylogeny -gt
  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.

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Tree Explorer

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

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• Identify orthologous and paralogous relationships

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• 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?

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NJ
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MP (out of 315 when using equally parsimonious
trees)
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MP Place a root in the same place in both trees.
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MP
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