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