PhyTree visualized on 197 (pid and score distance)

Input

1) PID distance
Aligner: SmithWaterman
ScoringMatrix: EDNAFULL
GapOpen: -16
GapExt: -4
DistanceType: (1-PercentIdentity)
WithReverse: Yes

2) Score distance
Aligner: SmithWaterman
ScoringMatrix: EDNAFULL
GapOpen: -16
GapExt: -4
DistanceType: (1-Normalized Score)
WithReverse: Yes

Visualization Algorithm 

DA-SMACOF

Result in Plot

1) Plot from PID distance

2) Plot from Score distance