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Retrieval from the Database of Pre-calcuated Genotyping/Subtyping Results

Virus: HIV-1 / Sequence Type: Nucleotide

Sequence Description: (Link to NCBI GenBank)

Multiple Substitution Correction Algorithm: Jukes-Cantor

All sites that include gaps were deleted.


Gene by Gene Subtype Prediction Summary

Gene Start Stop Length LANL Subtype Major Subtype Nested Analysis Final Decision
vif 108 185 71 B B B B (Major agrees Nested with high confidence)
5rev 182 248 54 B B B (Unambiguous Nested)
5tat 182 248 60 B B B (Unambiguous Nested)
3tat 251 342 91 B B B (Unambiguous Nested)
3rev 251 344 93 B B B (Unambiguous Nested)


Detailed result for vif (major) Outlierness: 0.494287 (all), 0.841834 (group)
Subtype Posterior Probability
01_AE 0.0000000000771088
A 0.00000996535
B 0.939851
C 0.0588308
D 0.000495301
F 0.00000000544873
G 0.000804564
H 0.000000000118128
J 0.000000881872
K 0.00000782295

Cross-Validation of Discriminant Models
Miss-Classification Rate: 79 / 945 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    49   3   0   0   0   0   1   0   0
    A         1  60   0   5   0   0   7   1   0
    B         0   1 354   5   6   1   0   0   3
    C         0   5   1 351   1   4   2   0   0
    D         0   0   8   5  35   0   0   0   0
    F         0   0   0   0   0  13   0   0   0
    G         0   9   0   5   0   0   3   0   0
    H         0   1   0   0   0   2   0   0   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   1   0   0   0   0   0   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vif (nested) Outlierness: 0.600945 (all), 0.89283 (group)
Subtype Posterior Probability
03_AB 0.00000873633
10_CD 0.000000000135186
12_BF 0.00000000482756
14_BG 0.00148193
15_01B 5.88187e-16
B 0.985258
C 0.0132515

Cross-Validation of Discriminant Models
Miss-Classification Rate: 30 / 753 at 10 Dimensional MDS
         Predicted
Objective 03_AB 10_CD 12_BF 14_BG 15_01B   B   C
   03_AB      0     0     0     0      0   0   0
   10_CD      0     2     0     0      0   0   1
   12_BF      0     0     7     0      0   2   0
   14_BG      0     0     0     0      0   3   0
   15_01B     0     0     0     0      3   0   0
   B          6     0     3     4      0 351   6
   C          0     0     1     0      1   2 360

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5rev (major) Outlierness: 0.975149 (all), 0.921511 (group)
Subtype Posterior Probability
01_AE 7.39056e-16
A 0.00000000000223052
B 1
C 0.0000000000876048
D 0.00000012278
F 0.000000121823
G 5.3252e-17
H 3.6106e-29
J 3.47685e-17
K 0.0000000000000989847

Cross-Validation of Discriminant Models
Miss-Classification Rate: 57 / 703 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    48   3   0   1   0   0   6   0   0   0
    A         4  48   0   7   0   0   2   0   0   0
    B         0   0 150   2   2   0   0   0   0   0
    C         0   5   0 344   0   1   0   0   0   0
    D         0   1   4   0  40   1   0   0   0   0
    F         0   1   0   2   1   7   0   0   0   1
    G         3   5   0   1   0   0   7   0   0   0
    H         0   1   0   0   0   0   0   2   0   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   1   0   0   1   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5rev (nested) Outlierness: 0.885221 (all), 0.88821 (group)
Subtype Posterior Probability
03_AB 0.00000923683
07_BC 4.02524e-17
08_BC 0.0000000151531
12_BF 0.000192694
14_BG 0.0000000000000483927
15_01B 0.0000000000000151218
B 0.999798

Cross-Validation of Discriminant Models
Miss-Classification Rate: 16 / 173 at 10 Dimensional MDS
         Predicted
Objective 08_BC 12_BF 15_01B   B
   03_AB      0     0      0   0
   07_BC      0     0      0   0
   08_BC      2     0      0   0
   12_BF      0     4      0   5
   14_BG      0     0      2   0
   15_01B     0     0      4   0
   B          1     6      0 147

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (major) Outlierness: 0.702955 (all), 0.820029 (group)
Subtype Posterior Probability
01_AE 0.0000000000000142026
A 0.0000000000556045
B 0.999997
C 0.000000000120909
D 0.000000257196
F 0.00000229283
G 2.10712e-16
H 6.81968e-30
J 2.03536e-16
K 0.00000000000348948

Cross-Validation of Discriminant Models
Miss-Classification Rate: 45 / 659 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    40   7   0   0   0   0   5   0   1
    A         4  55   0   1   0   0   3   0   0
    B         0   1 156   1   1   0   0   0   0
    C         0   0   1 306   0   0   0   0   0
    D         0   0   4   0  37   2   0   0   1
    F         0   0   0   2   0   9   0   0   1
    G         3   3   0   1   0   0   8   0   0
    H         0   1   0   0   0   0   0   2   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   1   0   0   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (nested) Outlierness: 0.681931 (all), 0.647081 (group)
Subtype Posterior Probability
03_AB 0.0000608953
07_BC 5.0639e-17
08_BC 0.00000612383
12_BF 0.00147493
14_BG 6.24947e-17
15_01B 0.00000000000000141658
B 0.998458

Cross-Validation of Discriminant Models
Miss-Classification Rate: 17 / 176 at 10 Dimensional MDS
         Predicted
Objective 12_BF 14_BG 15_01B   B
   03_AB      0     0      0   0
   07_BC      0     0      0   0
   08_BC      0     0      0   0
   12_BF      4     0      0   6
   14_BG      0     1      1   0
   15_01B     0     0      2   0
   B          7     0      0 152

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 3tat (major) Outlierness: 0.488078 (all), 0.763902 (group)
Subtype Posterior Probability
01_AE 2.65573e-20
A 0.00000000356847
B 0.999876
C 0.0000197374
D 0.000103441
F 0.000000279661
G 1.27264e-16
H 0.00000000039436
J 1.03468e-17
K 0.000000478334

Cross-Validation of Discriminant Models
Miss-Classification Rate: 24 / 659 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J
    01_AE    50   0   0   0   0   0   3   0   0
    A         0  59   0   3   0   0   0   0   1
    B         0   0 156   0   2   0   0   1   0
    C         0   1   0 305   0   1   0   0   0
    D         0   0   0   0  44   0   0   0   0
    F         0   0   0   5   0   7   0   0   0
    G         2   0   0   0   0   0  13   0   0
    H         0   0   0   1   0   1   0   1   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   1   0   1   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 3tat (nested) Outlierness: 0.380424 (all), 0.519892 (group)
Subtype Posterior Probability
03_AB 0.000224243
07_BC 0.0000000000957165
08_BC 2.60035e-28
12_BF 0.0000917506
14_BG 0.00000000000000383521
15_01B 2.33972e-27
B 0.999684

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 176 at 10 Dimensional MDS
         Predicted
Objective 03_AB 12_BF 14_BG 15_01B   B
   03_AB      0     0     0      0   0
   07_BC      0     0     0      0   0
   08_BC      0     0     0      0   0
   12_BF      0     8     0      0   2
   14_BG      0     0     2      0   0
   15_01B     0     0     0      2   0
   B          1     0     0      0 158

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 3rev (major) Outlierness: 0.495674 (all), 0.602394 (group)
Subtype Posterior Probability
01_AE 1.61313e-20
A 0.00000000138122
B 0.999905
C 0.0000136903
D 0.0000810797
F 0.000000099077
G 3.37405e-17
H 0.000000000202742
J 4.39072e-17
K 0.000000138514

Cross-Validation of Discriminant Models
Miss-Classification Rate: 21 / 703 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    55   0   0   0   0   0   3   0   0   0
    A         0  59   0   1   0   0   0   0   1   0
    B         0   0 151   0   3   0   0   0   0   0
    C         0   1   0 348   0   1   0   0   0   0
    D         0   0   0   0  46   0   0   0   0   0
    F         0   0   0   4   0   8   0   0   0   0
    G         2   0   0   0   0   0  14   0   0   0
    H         0   0   0   1   0   0   0   1   0   1
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   1   0   1   0   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 3rev (nested) Outlierness: 0.381133 (all), 0.508637 (group)
Subtype Posterior Probability
03_AB 0.000318462
07_BC 0.0000000000387285
08_BC 1.8991e-22
12_BF 0.00000752867
14_BG 6.16891e-17
15_01B 1.39799e-23
B 0.999674

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 173 at 10 Dimensional MDS
         Predicted
Objective 03_AB 08_BC 12_BF 14_BG 15_01B   B
   03_AB      0     0     0     0      0   0
   07_BC      0     0     0     0      0   0
   08_BC      0     2     0     0      0   0
   12_BF      0     0     8     0      0   1
   14_BG      0     0     0     2      0   0
   15_01B     0     0     0     1      3   0
   B          2     0     0     0      0 152

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Copyrighted by Bio-Data Mining Lab, Department of Bioinformatics and Life Sciences, Soongsil University, Seoul, Korea