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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 117 1645 963 ? B B B (Unambiguous Nested)
pol 1433 4449 2227 B B B (Unambiguous Nested)
vif 4393 4972 522 B B B (Unambiguous Nested)
vpr 4911 5202 147 B B B (Unambiguous Nested)
5tat 5182 5393 178 B B B (Major agrees Nested with high confidence)
vpu 5523 5644 52 01_AE 03_AB Undecided
env 6152 8152 1247 B B Undecided
nef 8153 8781 246 B B Undecided
ltr 8442 8894 256 B B Undecided


Detailed result for gag (major) Outlierness: 0.988307 (all), 1.95147 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 7.54236e-31
F 0
G 0
H 0
J 1.00367e-39
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: 1.19875 (all), 1.18447 (group)
Subtype Posterior Probability
03_AB 0
07_BC 0
08_BC 0
12_BF 2.61788e-34
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: 0.954825 (all), 0.962418 (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 / 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  12   0   0   0
    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: 1.31532 (all), 1.32156 (group)
Subtype Posterior Probability
03_AB 4.9377e-17
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: 5 / 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      8      0   1
   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: 0.6949 (all), 0.629519 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 1.96176e-25
F 9.23456e-43
G 4.94658e-43
H 2.39083e-24
J 3.67381e-28
K 3.64799e-25

Cross-Validation of Discriminant Models
Miss-Classification Rate: 15 / 945 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J
    01_AE    53   0   0   0   0   0   0   0   0
    A         0  69   0   0   0   0   5   0   0
    B         0   0 370   0   0   0   0   0   0
    C         0   0   0 364   0   0   0   0   0
    D         0   0   0   0  47   0   0   1   0
    F         0   0   0   0   0  10   0   3   0
    G         0   1   0   0   0   0  16   0   0
    H         0   0   0   0   0   0   0   1   2
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   2   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vif (nested) Outlierness: 0.798143 (all), 0.823137 (group)
Subtype Posterior Probability
03_AB 0.0000530656
12_BF 3.80465e-39
14_BG 0
15_01B 0
B 0.999947

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: 0.858416 (all), 0.889292 (group)
Subtype Posterior Probability
01_AE 6.41571e-17
A 5.62714e-22
B 0.999839
C 1.64437e-19
D 0.000161396
F 0.000000000000223039
G 9.54196e-22
H 0.0000000000146889
J 4.2923e-16
K 0.0000000000000706337

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 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  55   0   0   0   0   0   0   0
    B         0   0 283   0   1   0   0   1   0
    C         0   0   0 364   0   0   0   0   0
    D         0   0   1   0  43   0   0   0   0
    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   1   0   2   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 vpr (nested) Outlierness: 0.994059 (all), 0.994278 (group)
Subtype Posterior Probability
03_AB 0.000133167
07_BC 3.31879e-20
08_BC 1.2953e-39
12_BF 0.000000000000494708
14_BG 7.10905e-23
15_01B 1.97052e-34
B 0.999867

Cross-Validation of Discriminant Models
Miss-Classification Rate: 10 / 300 at 10 Dimensional MDS
         Predicted
Objective 07_BC 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     6     0      0   2
   14_BG      0     0     0      0   0
   15_01B     0     0     2      1   0
   B          1     1     0      0 283

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (major) Outlierness: 1.10048 (all), 1.61583 (group)
Subtype Posterior Probability
01_AE 2.78099e-33
A 4.23354e-28
B 0.999999
C 8.83846e-35
D 0.00000060414
F 1.95368e-31
G 6.07133e-23
H 1.24364e-30
J 2.71321e-23
K 2.12869e-22

Cross-Validation of Discriminant Models
Miss-Classification Rate: 18 / 659 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    52   1   0   0   0   0   0   0   0   0
    A         7  52   1   0   0   0   3   0   0   0
    B         0   0 159   0   0   0   0   0   0   0
    C         0   0   0 307   0   0   0   0   0   0
    D         0   0   0   0  44   0   0   0   0   0
    F         0   0   0   0   0  10   0   0   0   2
    G         0   1   0   0   0   0  14   0   0   0
    H         0   0   0   0   0   0   0   3   0   0
    J         0   0   0   0   0   0   0   0   0   0
    K         1   0   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: 2.68144 (all), 2.69577 (group)
Subtype Posterior Probability
03_AB 0.0000000607472
07_BC 6.09888e-20
08_BC 1.81648e-28
12_BF 0.000000000000182199
14_BG 8.12733e-32
15_01B 2.63945e-36
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 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      7     0      0   3
   14_BG      0     2      0   0
   15_01B     0     0      2   0
   B          0     0      0 159

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpu (major) Outlierness: 3.73567 (all), 18.6531 (group)
Subtype Posterior Probability
01_AE 0.582249
A 0.0000000000000636226
B 0.417751
C 1.60031e-38
D 0.000000000318072
F 2.73314e-19
G 0.000000000000115472
H 1.63374e-16
J 8.74953e-25
K 2.44968e-34

Cross-Validation of Discriminant Models
Miss-Classification Rate: 162 / 932 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE     3   1  40   0   0   2   0   0   0   0
    A         0  22  43   3   1   0   0   1   0   0
    B         6  12 295   0   0   3   3   2   0   0
    C         0   6   1 388   2   0   0   0   0   0
    D         1   3  11   2  35   1   1   0   0   0
    F         0   0   4   0   0   8   0   0   0   0
    G         1   1   3   0   0   1  14   0   0   2
    H         0   2   1   0   0   0   0   3   0   0
    J         0   0   0   0   0   0   0   0   2   0
    K         0   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 vpu (nested) Outlierness: 5.76135 (all), 3.4e38 (group)
Subtype Posterior Probability
01_AE 0.000000856629
03_AB 0.996866
08_BC 4.08689e-16
11_cpx 0.00000000000000614866
12_BF 0.000000100144
13_cpx 7.58622e-36
14_BG 1.68115e-22
15_01B 0.000174612
B 0.00295832

Cross-Validation of Discriminant Models
Miss-Classification Rate: 78 / 398 at 10 Dimensional MDS
         Predicted
Objective 01_AE 11_cpx 12_BF 13_cpx 14_BG 15_01B   B
   01_AE      4      1     0      0     0      0  41
   03_AB      0      0     0      0     0      0   0
   08_BC      0      0     0      0     0      0   0
   11_cpx     1      5     0      1     0      0   2
   12_BF      0      0     0      0     0      0  12
   13_cpx     1      0     0      2     0      0   0
   14_BG      0      0     0      1     2      0   0
   15_01B     0      0     0      0     0      0   2
   B          7      5     1      0     0      1 307

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (major) Outlierness: 2.28847 (all), 7.28819 (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: 7.73212 (all), 8.0548 (group)
Subtype Posterior Probability
03_AB 3.70985e-22
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: 13 / 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      9     1     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      7 447

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for nef (major) Outlierness: 1.72028 (all), 2.44878 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 2.7094e-20
F 0
G 0
H 0
J 0
K 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 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         0 108   0   0   0   0   0   0   1   0
    B         0   0 766   0   0   0   0   0   0   0
    C         1   0   0 496   0   0   0   0   0   0
    D         0   0   0   0  80   0   0   0   0   0
    F         0   0   0   0   0  11   0   1   0   1
    G         0   0   0   0   0   0  34   0   1   1
    H         0   0   0   0   0   0   1   6   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 nef (nested) Outlierness: 2.0222 (all), 2.09332 (group)
Subtype Posterior Probability
03_AB 0
07_BC 0
08_BC 0
12_BF 1.28053e-32
14_BG 0
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      5     0      0   3
   14_BG      0    14      0   0
   15_01B     0     0      4   0
   B          0     0      0 766

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for ltr (major) Outlierness: 2.55646 (all), 8.13423 (group)
Subtype Posterior Probability
01_AE 0
A 2.01191e-38
B 1
C 0
D 1.02221e-39
F 0
G 0
H 1.52742e-42
J 0
K 0

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: 5.81807 (all), 9.25599 (group)
Subtype Posterior Probability
03_AB 0
07_BC 0
08_BC 0
12_BF 0
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 1 / 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     1     1     0  0
    08_BC     0     0     5     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