Monday, September 24, 2012

Phy Tree on Side Plot


Environment: Tempest; 32 nodes (768 cores)
Aligner: SmithWaterman
ScoringMatrix: EDNAFULL
GapOpen: -16
GapExt: -4
DistanceType: (1-Normalized Score*), Percentage Identity
Method: 1291+123+74+420 all varied
WithReverse: dynamic determine algorithm


1) 1291 new GenBank sequences; (id:617~1907)
2) 123 consensus sequence; (id: 420~542)
3) 74 sequences from Gen Bank; (id: 543~616)
4) 420 center sequences; (id: 0~419)

Tree Configuration

New sequences from Gen Bank: Hexagon
Consensus sequence in Haixu 123: Triangle
Center sequences in 420: original points
Root: Sphere
Color Scheme:  1) Phylogenetic tree generated here
               2) Mega Region coloring

Final Result

Phylogenetic tree coloring:

1. Plot File in PVIZ format, with pid distance.
2. Plot File in PVIZ format, with old* score distance.

Mega Region coloring:

3. Plot File in PVIZ format, with old* score distance.

Screen Shot

1. pid distance

2. old* score distance

3. old* score distance with mega region

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