Length Checking On PID and Score Matrices

Input

1) PID distance
Aligner: SmithWaterman
ScoringMatrix: EDNAFULL
GapOpen: -16
GapExt: -4
DistanceType: (1-PercentIdentity)
WithReverse: No

2) Score distance
Aligner: SmithWaterman
ScoringMatrix: EDNAFULL
GapOpen: -16
GapExt: -4
DistanceType: (1-Normalized Score)
WithReverse: No

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

Visualization Algorithm 

DA-SMACOF

Configuration

Original Sequence Lengths
Cluster 4: 200~249
Cluster 5: 250~299
Cluster 6: 300~349
Cluster 7: 350~399
Cluster 8: 400~449
Cluster 9: 450~499
Cluster 10: 500~549
Cluster 11: 550~599
Cluster 12: 600~649
Cluster 13: 650~699
Cluster 14: 700~749
Cluster 16: 800~849
Cluster 20: 1050~1099

Result in Plot

1) PID distance without Reverse

2) Score distance without Reverse

3) Score distance with Reverse