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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 441 1947 963 06_cpx A 06_cpx 06_cpx (Unambiguous Nested)
pol 1739 4751 2703 J 06_cpx Undecided
vif 4695 5274 522 J 06_cpx 06_cpx (Unambiguous Nested)
vpr 5213 5504 147 F F Undecided
5tat 5484 5695 185 K 06_cpx 06_cpx (Unambiguous Nested)
vpu 5737 5970 95 G 06_cpx Undecided
env 5887 8413 1588 G 06_cpx Undecided
nef 8414 9038 246 G 06_cpx Undecided
ltr 8706 9224 256 J 06_cpx Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
89116506 ABD61768 gag 35 498 337 A 06_cpx 06_cpx (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.950836 (all), 0.597365 (group)
Subtype Posterior Probability
01_AE 4.51682e-25
A 1
B 0
C 0
D 0
F 0
G 5.51134e-09
H 5.20512e-09
J 7.2502e-16
K 1.40361e-36

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 (all), 1 (group)
Subtype Posterior Probability
02_AG 0
03_AB 7.63387e-40
04_cpx 9.33095e-32
06_cpx 1
09_cpx 0
11_cpx 0
13_cpx 0
16_A2D 0
A 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 225 at 10 Dimensional MDS
         Predicted
Objective 02_AG 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 16_A2D   A
   02_AG     58      0      0      0      0      0      0   1
   03_AB      0      0      0      0      0      0      0   0
   04_cpx     0      3      0      0      0      0      0   0
   06_cpx     0      0      9      0      0      0      0   0
   09_cpx     0      0      0      5      0      0      0   0
   11_cpx     0      0      0      0     10      0      0   0
   13_cpx     0      0      0      0      0      3      0   0
   16_A2D     0      0      0      0      0      0      2   0
   A          0      0      0      0      0      1      4 128

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (major) Outlierness: 0.633372 (all), 3.4e+38 (group)
Subtype Posterior Probability
01_AE 0
A 1.76283e-42
B 0
C 0
D 0
F 3.29207e-36
G 5.55066e-40
H 9.08053e-06
J 0.999647
K 0.000343728

Cross-Validation of Discriminant Models
Miss-Classification Rate: 4 / 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  10   0   0   2
    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: 1.14656 (all), 4.27464 (group)
Subtype Posterior Probability
06_cpx 1
11_cpx 0
13_cpx 0
J 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 1 / 19 at 10 Dimensional MDS
         Predicted
Objective 06_cpx 11_cpx 13_cpx
   06_cpx      5      0      0
   11_cpx      0     10      0
   13_cpx      0      0      3
   J           0      0      0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vif (major) Outlierness: 0.643004 (all), 3.4e+38 (group)
Subtype Posterior Probability
01_AE 1.42155e-31
A 7.68854e-21
B 3.04698e-16
C 9.41083e-18
D 2.29669e-31
F 2.36429e-05
G 1.76741e-18
H 0.27709
J 0.495321
K 0.227566

Cross-Validation of Discriminant Models
Miss-Classification Rate: 13 / 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  70   0   0   0   0   4   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   2   1
    G         0   1   0   0   0   0  16   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   2   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vif (nested) Outlierness: 1.09224 (all), 1.80867 (group)
Subtype Posterior Probability
04_cpx 0
06_cpx 1
11_cpx 0
13_cpx 5.15479e-37
H 0
J 5.75233e-42
K 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 2 / 24 at 10 Dimensional MDS
         Predicted
Objective 04_cpx 06_cpx 11_cpx 13_cpx H J K
   04_cpx      3      0      0      0 0 0 0
   06_cpx      0      3      0      0 0 0 0
   11_cpx      0      0      9      0 0 0 0
   13_cpx      0      0      0      3 0 0 0
   H           0      0      0      0 2 1 0
   J           0      0      0      0 0 0 0
   K           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 (major) Outlierness: 0.764693 (all), 2.68887 (group)
Subtype Posterior Probability
01_AE 0.00253926
A 1.2938e-06
B 0.00117288
C 2.79284e-20
D 8.80827e-10
F 0.99574
G 1.86656e-05
H 2.81896e-07
J 0.000122686
K 0.000404954

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: 2.01953 (all), 5.16077 (group)
Subtype Posterior Probability
05_DF 1.05035e-07
12_BF 0.294614
F 0.705386

Cross-Validation of Discriminant Models
Miss-Classification Rate: 13 / 20 at 10 Dimensional MDS
         Predicted
Objective 05_DF 12_BF F
    05_DF     1     1 1
    12_BF     0     3 5
    F         0     6 3

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (major) Outlierness: 0.916872 (all), 33.2468 (group)
Subtype Posterior Probability
01_AE 2.18692e-16
A 1.40744e-09
B 4.20878e-08
C 4.63922e-10
D 2.16311e-09
F 1.86971e-06
G 7.03083e-12
H 2.32548e-13
J 0.00267325
K 0.997325

Cross-Validation of Discriminant Models
Miss-Classification Rate: 11 / 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         1  59   1   0   0   0   2   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         1   0   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         0   0   0   0   0   0   0   0   2   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (nested) Outlierness: 1 (all), 1 (group)
Subtype Posterior Probability
04_cpx 0
06_cpx 1
K 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 4 / 11 at 7 Dimensional MDS
         Predicted
Objective 04_cpx 06_cpx K
   04_cpx      2      0 1
   06_cpx      2      3 1
   K           0      0 2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpu (major) Outlierness: 0.764305 (all), 1.22959 (group)
Subtype Posterior Probability
01_AE 5.44148e-15
A 1.057e-13
B 4.65269e-11
C 1.68241e-24
D 4.00443e-13
F 1.80379e-12
G 1
H 1.89894e-14
J 3.27933e-27
K 6.579e-17

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: 1.64121 (all), 3.06169 (group)
Subtype Posterior Probability
02_AG 6.20776e-09
04_cpx 8.84133e-32
06_cpx 0.942664
09_cpx 5.743e-17
11_cpx 4.65455e-25
13_cpx 2.42387e-18
14_BG 2.76301e-16
G 0.0573362

Cross-Validation of Discriminant Models
Miss-Classification Rate: 12 / 95 at 10 Dimensional MDS
         Predicted
Objective 02_AG 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 14_BG  G
   02_AG     43      0      0      0      0      0     0  3
   04_cpx     0      2      0      0      1      0     0  0
   06_cpx     0      0      5      0      0      0     0  0
   09_cpx     0      0      0      4      0      0     0  0
   11_cpx     1      0      0      0      7      1     0  0
   13_cpx     0      0      0      0      0      3     0  0
   14_BG      0      0      0      0      0      0     3  0
   G          3      0      2      0      0      0     1 16

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (major) Outlierness: 0.927411 (all), 2.04507 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 0
C 0
D 0
F 0
G 1
H 0
J 5.51147e-14
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: 1.05741 (all), 3.64196 (group)
Subtype Posterior Probability
02_AG 0
04_cpx 0
06_cpx 1
09_cpx 0
11_cpx 0
13_cpx 0
14_BG 0
G 1.01394e-33

Cross-Validation of Discriminant Models
Miss-Classification Rate: 0 / 108 at 10 Dimensional MDS
         Predicted
Objective 02_AG 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 14_BG  G
   02_AG     55      0      0      0      0      0     0  0
   04_cpx     0      3      0      0      0      0     0  0
   06_cpx     0      0      6      0      0      0     0  0
   09_cpx     0      0      0      4      0      0     0  0
   11_cpx     0      0      0      0     11      0     0  0
   13_cpx     0      0      0      0      0      3     0  0
   14_BG      0      0      0      0      0      0     3  0
   G          0      0      0      0      0      0     0 23

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for nef (major) Outlierness: 1.10971 (all), 3.48211 (group)
Subtype Posterior Probability
01_AE 9.73193e-11
A 4.60463e-10
B 0
C 7.68783e-05
D 0
F 1.01924e-09
G 0.838306
H 1.49842e-07
J 0.161617
K 5.87844e-10

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 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  35   0   1   0
    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: 1.368 (all), 5.07142 (group)
Subtype Posterior Probability
02_AG 5.35288e-38
04_cpx 4.04439e-28
06_cpx 0.99769
09_cpx 2.03691e-16
11_cpx 5.44763e-25
13_cpx 8.30491e-13
14_BG 3.85037e-25
G 2.11655e-24
J 0.00231044

Cross-Validation of Discriminant Models
Miss-Classification Rate: 17 / 147 at 10 Dimensional MDS
         Predicted
Objective 02_AG 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 14_BG  G  J
   02_AG     69      0      0      0      0      0     0  0  0
   04_cpx     0      3      0      0      0      0     0  0  0
   06_cpx     0      0      9      0      0      1     0  0  1
   09_cpx     0      0      0      3      0      0     0  0  0
   11_cpx     0      0      0      0      5      1     0  0  0
   13_cpx     0      0      0      0      1      2     0  0  0
   14_BG      0      0      0      0      0      0     7  7  0
   G          1      0      0      0      0      0     3 32  0
   J          0      0      2      0      0      0     0  0  0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for ltr (major) Outlierness: 1.41269 (all), 17.2351 (group)
Subtype Posterior Probability
01_AE 6.28042e-16
A 4.28101e-14
B 6.30205e-21
C 4.43279e-06
D 1.88617e-38
F 6.00778e-12
G 3.19928e-24
H 2.54605e-09
J 0.805179
K 0.194816

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: 1.97897 (all), 5.37591 (group)
Subtype Posterior Probability
04_cpx 9.10424e-42
06_cpx 1
11_cpx 0
J 0
K 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 10 / 14 at 10 Dimensional MDS
         Predicted
Objective 04_cpx 06_cpx 11_cpx J K
   04_cpx      2      0      0 0 0
   06_cpx      2      0      0 1 1
   11_cpx      2      0      1 1 0
   J           1      0      0 1 0
   K           0      1      0 1 0

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