1 / 14

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.

laddie
Download Presentation

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

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related