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Phylogenetic ToolsTara 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
Do a BLAST (Basic Local Alignment Search Tool) search on the sequence
Choose sequences and Add to Alignment
Align Sequences
Make a tree Go back into main MEGA window
Several methods to choose from• Neighbor Joining• Maximum Likelihood• Maximum Parsimony• And more
Tree tools Different views
Root tree
View subtrees
Add captions
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
Mequite (Character Matrix)
Ancestral State Reconstruction
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.”
FigTree
FigTree
FigTree
Save or Export Tree Save as image (PDF, TIFF, or EMF)
Export as different file types
Save tree session
Diigo Page for Tools Used http://www.diigo.com/list/tarallk/
phylogenetic-tools