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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
gag 165 1675 963 ? B B B (Major agrees Nested with high confidence)
pol 1450 4478 2702 B B B (Unambiguous Nested)
vif 4422 4842 394 B B B (Unambiguous Nested)
vpr 5005 5231 116 B 03_AB Undecided
5tat 5211 5335 104 B B Undecided
vpu 5455 5688 95 B B B (Unambiguous Nested)
env 5605 8171 1578 B B Undecided
nef 8398 8793 182 B B B (Unambiguous Nested)
ltr 8461 8917 256 B B B (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 1.14265 (all), 1.45504 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 2.21039e-40
F 0
G 0
H 0
J 0
K 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 10 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    72   0   0   0   0   0   0   0   0
    A         0 129   0   1   0   0   1   2   0
    B         0   0 262   0   1   2   0   0   0
    C         0   0   0 552   0   0   0   1   0
    D         0   0   0   0  76   0   0   0   0
    F         0   0   0   0   0  14   0   0   1
    G         0   0   0   0   0   0  21   0   0
    H         0   0   0   0   0   0   0   3   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   0   3

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 7.73474 (all), 9.12584 (group)
Subtype Posterior Probability
03_AB 0
07_BC 0
08_BC 0
12_BF 0
14_BG 0
15_01B 0
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 290 at 10 Dimensional MDS
         Predicted
Objective 07_BC 08_BC 12_BF 15_01B   B
   03_AB      0     0     0      0   0
   07_BC      3     0     0      0   0
   08_BC      0     5     0      0   0
   12_BF      0     0     8      0   2
   14_BG      0     0     0      0   0
   15_01B     0     0     0      5   0
   B          0     0     2      0 263

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (major) Outlierness: 0.896262 (all), 0.587946 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 0
F 0
G 0
H 0
J 0
K 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 3 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    57   0   0   0   0   0   0   0   0
    A         0  58   0   1   0   0   0   0   0
    B         0   0 168   0   0   0   0   0   0
    C         0   0   0 371   0   0   0   0   0
    D         0   0   0   0  46   0   0   0   0
    F         0   0   0   0   0  11   0   0   1
    G         0   0   0   0   0   0  16   0   0
    H         0   0   0   0   0   0   0   3   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   0   2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 0.731999 (all), 0.702917 (group)
Subtype Posterior Probability
03_AB 0.00000000000820973
07_BC 0
08_BC 0
12_BF 0
14_BG 0
15_01B 0
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 4 / 184 at 10 Dimensional MDS
         Predicted
Objective 12_BF 15_01B   B
   03_AB      0      0   0
   07_BC      0      0   0
   08_BC      0      0   0
   12_BF      9      0   0
   14_BG      0      0   0
   15_01B     0      3   0
   B          0      0 168

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vif (major) Outlierness: 0.602844 (all), 0.670433 (group)
Subtype Posterior Probability
01_AE 0
A 6.30773e-38
B 1
C 5.2226e-35
D 8.8098e-20
F 1.2693e-30
G 1.55154e-34
H 0.00000000000000138857
J 1.5254e-21
K 0.000000000000111753

Cross-Validation of Discriminant Models
Miss-Classification Rate: 12 / 945 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    53   0   0   0   0   0   0   0   0   0
    A         0  70   0   0   0   0   4   0   0   0
    B         0   0 370   0   0   0   0   0   0   0
    C         0   0   0 364   0   0   0   0   0   0
    D         0   0   0   0  47   0   0   0   1   0
    F         0   0   0   0   0  10   0   0   3   0
    G         0   2   0   0   0   0  15   0   0   0
    H         0   0   0   0   0   0   0   2   1   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   0   0   2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vif (nested) Outlierness: 0.766243 (all), 0.732045 (group)
Subtype Posterior Probability
03_AB 0.00000849534
12_BF 2.81121e-40
14_BG 6.66432e-38
15_01B 0
B 0.999991

Cross-Validation of Discriminant Models
Miss-Classification Rate: 2 / 386 at 10 Dimensional MDS
         Predicted
Objective 03_AB 12_BF 14_BG 15_01B   B
   03_AB      0     0     0      0   0
   12_BF      0     9     0      0   0
   14_BG      0     0     3      0   0
   15_01B     0     0     0      3   0
   B          1     0     0      0 369

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpr (major) Outlierness: 1.75495 (all), 3.04288 (group)
Subtype Posterior Probability
01_AE 2.05809e-26
A 2.3419e-37
B 0.999719
C 1.28438e-34
D 0.000281096
F 8.01666e-28
G 3.3405e-27
H 1.75951e-27
J 2.01503e-18
K 3.69234e-29

Cross-Validation of Discriminant Models
Miss-Classification Rate: 8 / 810 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    31   0   0   0   0   0   0   0   0
    A         1  54   0   0   0   1   0   0   0
    B         0   0 284   0   0   1   0   0   0
    C         0   0   0 364   0   0   0   0   0
    D         0   0   1   0  42   0   0   0   1
    F         0   0   0   0   0   9   0   0   0
    G         1   0   0   0   0   0  14   0   0
    H         0   0   0   0   0   0   0   2   1
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   0   2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpr (nested) Outlierness: 4.71891 (all), 3.4e38 (group)
Subtype Posterior Probability
03_AB 0.99854
07_BC 4.10366e-18
08_BC 1.4013e-45
12_BF 0.000000000000174221
14_BG 1.98786e-34
15_01B 0
B 0.00146005

Cross-Validation of Discriminant Models
Miss-Classification Rate: 9 / 300 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      6     0      0   2
   14_BG      0     0      0   0
   15_01B     0     2      1   0
   B          1     0      0 284

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (major) Outlierness: 1.41479 (all), 2.24684 (group)
Subtype Posterior Probability
01_AE 5.7966e-26
A 1.69337e-17
B 1
C 3.66284e-23
D 0.0000000964159
F 2.9431e-18
G 8.35332e-18
H 0.0000000000000665094
J 3.52572e-19
K 5.91023e-18

Cross-Validation of Discriminant Models
Miss-Classification Rate: 20 / 659 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    53   0   0   0   0   0   0   0   0
    A         6  51   1   2   0   0   1   0   2
    B         0   0 159   0   0   0   0   0   0
    C         0   1   0 306   0   0   0   0   0
    D         0   0   1   0  43   0   0   0   0
    F         0   0   0   0   0   9   0   3   0
    G         0   0   0   0   0   0  15   0   0
    H         0   0   0   0   0   0   0   3   0
    J         0   0   0   0   0   0   0   0   0
    K         1   0   0   0   0   0   0   1   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (nested) Outlierness: 2.03211 (all), 2.14965 (group)
Subtype Posterior Probability
03_AB 0.0000000186882
07_BC 0.00827369
08_BC 1.26894e-16
12_BF 0.0000000118482
14_BG 3.62729e-20
15_01B 4.3256e-29
B 0.991726

Cross-Validation of Discriminant Models
Miss-Classification Rate: 8 / 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     7     0      0   3
   14_BG      0     0     2      0   0
   15_01B     0     0     0      2   0
   B          2     0     0      0 157

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpu (major) Outlierness: 1.02059 (all), 1.19655 (group)
Subtype Posterior Probability
01_AE 1.69394e-17
A 1.57842e-18
B 1
C 1.53821e-19
D 0.000000000569882
F 0.00000000000000263235
G 2.87731e-20
H 6.35771e-18
J 2.04415e-28
K 1.08426e-29

Cross-Validation of Discriminant Models
Miss-Classification Rate: 13 / 932 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J
    01_AE    44   2   0   0   0   0   0   0   0
    A         3  64   1   0   0   0   0   2   0
    B         0   0 321   0   0   0   0   0   0
    C         0   0   0 397   0   0   0   0   0
    D         0   0   0   0  54   0   0   0   0
    F         0   0   0   0   0  12   0   0   0
    G         0   0   0   0   0   0  22   0   0
    H         0   3   0   0   0   0   0   3   0
    J         0   0   0   0   0   0   0   0   2
    K         0   0   0   0   0   1   1   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpu (nested) Outlierness: 1.5487 (all), 1.53518 (group)
Subtype Posterior Probability
03_AB 0.00242385
08_BC 2.29929e-27
12_BF 0.0018874
14_BG 3.40087e-35
15_01B 0.00000000000000235845
B 0.995689

Cross-Validation of Discriminant Models
Miss-Classification Rate: 15 / 340 at 10 Dimensional MDS
         Predicted
Objective 12_BF 14_BG 15_01B   B
   03_AB      0     0      0   0
   08_BC      0     0      0   0
   12_BF      0     0      0  12
   14_BG      0     3      0   0
   15_01B     0     0      2   0
   B          1     0      0 320

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (major) Outlierness: 4.09335 (all), 12.6112 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 0
F 0
G 0
H 0
J 0
K 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 2 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    70   0   0   0   0   0   0   0   0
    A         0  82   0   0   0   0   0   0   0
    B         0   0 454   0   0   0   0   0   0
    C         0   0   0 464   0   0   0   0   0
    D         0   0   0   0  60   0   0   0   0
    F         0   0   0   0   0  15   0   0   1
    G         0   0   0   0   0   0  23   0   0
    H         0   0   0   0   0   0   0   3   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   0   2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 16.0303 (all), 17.6473 (group)
Subtype Posterior Probability
03_AB 5.88123e-31
07_BC 0
08_BC 0
12_BF 0
14_BG 2.6975e-42
15_01B 0
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 15 / 484 at 10 Dimensional MDS
         Predicted
Objective 07_BC 08_BC 12_BF 14_BG 15_01B   B
   03_AB      0     0     0     0      0   0
   07_BC      8     2     0     0      0   0
   08_BC      2     0     0     0      0   0
   12_BF      0     0     8     0      0   2
   14_BG      0     0     0     3      0   0
   15_01B     0     0     0     0      4   0
   B          0     0     0     0      8 446

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for nef (major) Outlierness: 0.632163 (all), 0.695878 (group)
Subtype Posterior Probability
01_AE 8.48653e-32
A 9.72297e-18
B 1
C 6.58841e-22
D 0.0000000017036
F 0.0000000000000205763
G 3.7923e-28
H 3.15228e-16
J 3.0043e-27
K 6.55935e-25

Cross-Validation of Discriminant Models
Miss-Classification Rate: 18 / 1559 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    47   0   0   0   0   0   0   0   0   0
    A         0 103   0   0   0   4   0   1   1   0
    B         0   0 766   0   0   0   0   0   0   0
    C         0   0   1 496   0   0   0   0   0   0
    D         0   0   2   0  78   0   0   0   0   0
    F         0   1   1   1   0   9   0   1   0   0
    G         0   0   0   0   0   0  35   0   0   1
    H         0   0   0   1   0   0   0   6   0   0
    J         0   0   0   0   0   0   0   0   0   2
    K         0   0   0   0   0   0   0   0   1   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for nef (nested) Outlierness: 0.672296 (all), 0.657666 (group)
Subtype Posterior Probability
03_AB 9.57817e-29
07_BC 1.28722e-31
08_BC 5.15818e-42
12_BF 0.00000000129347
14_BG 8.1329e-34
15_01B 0
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 795 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      6     0      0   2
   14_BG      0    14      0   0
   15_01B     0     0      4   0
   B          1     0      0 765

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for ltr (major) Outlierness: 0.532265 (all), 0.820867 (group)
Subtype Posterior Probability
01_AE 9.36799e-28
A 0.0000000000000013476
B 1
C 4.13911e-18
D 0.0000000000000254768
F 6.91586e-22
G 1.79681e-29
H 0.0000000000120448
J 5.62034e-25
K 0.00000000000000884999

Cross-Validation of Discriminant Models
Miss-Classification Rate: 3 / 276 at 10 Dimensional MDS
         Predicted
Objective 01_AE  A  B  C  D  F  G  H  J  K
    01_AE    52  0  0  0  0  0  0  0  0  0
    A         0 24  0  0  0  0  1  0  0  0
    B         0  0 62  0  0  0  0  0  0  0
    C         0  0  0 74  0  0  0  0  0  1
    D         0  0  0  0 38  0  0  0  0  0
    F         0  0  0  0  0  8  0  0  0  0
    G         0  0  0  0  0  0  9  0  0  0
    H         0  1  0  0  0  0  0  2  0  0
    J         0  0  0  0  0  0  0  0  2  0
    K         0  0  0  0  0  0  0  0  0  2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for ltr (nested) Outlierness: 0.616873 (all), 0.664927 (group)
Subtype Posterior Probability
03_AB 8.09156e-33
07_BC 4.04579e-32
08_BC 2.36772e-32
12_BF 4.76496e-26
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 3 / 74 at 10 Dimensional MDS
         Predicted
Objective 03_AB 07_BC 08_BC 12_BF  B
    03_AB     2     0     0     0  0
    07_BC     0     0     2     0  0
    08_BC     0     1     4     0  0
    12_BF     0     0     0     3  0
    B         0     0     0     0 62

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