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Phylogenetic Tools

Phylogenetic Tools. Tara and Pawel. Concept Map. Start with Known Sequence. Download MEGA (Molecular Evolutionary Genetics Analysis) http://www.megasoftware.net/. Use MEGA Web Browser to Find Related Sequences. Go to Align, Open Web browser

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Phylogenetic Tools

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  1. Phylogenetic Tools Tara and Pawel

  2. Concept Map

  3. Start with Known Sequence Download MEGA (Molecular Evolutionary Genetics Analysis) http://www.megasoftware.net/

  4. Use MEGA Web Browser to Find Related Sequences Go to Align, Open Web browser Do a BLAST (Basic Local Alignment Search Tool) search on the sequence Choose sequences and Add to Alignment

  5. Align Sequences

  6. Make a tree • Go back into main MEGA window • Several methods to choose from • Neighbor Joining • Maximum Likelihood • Maximum Parsimony • And more

  7. Tree tools Different views Root tree View subtrees Add captions

  8. Finished Tree

  9. Mequite (Character Matrix)

  10. Ancestral State Reconstruction

  11. Make Trees Pretty Program Description: “FigTreeis designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST.”

  12. FigTree

  13. FigTree

  14. FigTree

  15. Save or Export Tree Save as image (PDF, TIFF, or EMF) Export as different file types Save tree session

  16. Diigo Page for Tools Used http://www.diigo.com/list/tarallk/phylogenetic-tools

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