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Phylogenetic Tools Tara and Pawel

Tara and Pawel. Download MEGA (Molecular Evolutionary Genetics Analysis)

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Page 1: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)

Phylogenetic ToolsTara and Pawel

Page 2: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)

Concept Map

Page 3: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)

Start with Known Sequence

Download MEGA (Molecular Evolutionary Genetics Analysis)

http://www.megasoftware.net/

Page 4: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)

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

Page 5: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)
Page 6: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)

Align Sequences

Page 7: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)

Make a tree Go back into main MEGA window

Several methods to choose from• Neighbor Joining• Maximum Likelihood• Maximum Parsimony• And more

Page 8: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)
Page 9: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)
Page 10: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)

Tree tools Different views

Root tree

View subtrees

Add captions

Page 11: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)
Page 12: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)

Finished Tree T. vetulus RNASE1B

T. vetulus RNASE1C

T. johnii RNASE1B

T. phayrei RNASE1B

P. nemaeus RNASE1B

C. polykomos RNASE1B

R. bieti RNASE1B

R. avunculus RNASE1B

R. roxellana RNASE1B

R. avunculus RNASE1

T. phayrei RNASE1

T. johnii RNASE1

T. vetulus RNASE1

P. nemaeus RNASE1

C. polykomos RNASE1

M. mulatta RNASE1

67

99

46

96

77

72

42

38

49

68

14

22

58

0.008902

0.023329

0.015962

0.002480

0.014161

0.003003

-0.000042

0.004157

0.002168

0.001928

-0.000044

0.003888

0.002595

0.000198

0.004338

-0.000080

0.000107

0.013606

0.000044

0.005959

0.003116

0.005133

0.001974

0.003486

0.006274

0.000376

0.003509

0.001355

0.000299

0.003892

Page 13: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)

Mequite (Character Matrix)

Page 14: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)

Ancestral State Reconstruction

Page 15: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)

Make Trees Pretty Program Description:

“FigTree is 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.”

Page 16: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)

FigTree

Page 17: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)

FigTree

Page 18: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)

FigTree

Page 19: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)

Save or Export Tree Save as image (PDF, TIFF, or EMF)

Export as different file types

Save tree session

Page 20: Tara and Pawel.  Download MEGA (Molecular Evolutionary Genetics Analysis)

Diigo Page for Tools Used http://www.diigo.com/list/tarallk/

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