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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 116 1223 807 ? B B B (Unambiguous Nested)
pol 2011 4423 2273 B B Undecided
vif 4367 4946 522 B 03_AB Undecided
vpr 4885 5176 147 B B Undecided
5tat 5156 5367 185 B 03_AB Undecided
vpu 5400 5540 78 B B Undecided
nef 8125 8743 246 B B B (Major agrees Nested with high confidence)
ltr 8411 8864 256 B B B (Major agrees Nested with high confidence)


Detailed result for gag (major) Outlierness: 0.635095 (all), 0.717097 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 2.09109e-40
D 4.76663e-17
F 4.58316e-34
G 0
H 2.58197e-30
J 9.13049e-23
K 1.1799e-27

Cross-Validation of Discriminant Models
Miss-Classification Rate: 15 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    72   0   0   0   0   0   0   0   0   0
    A         0 127   0   1   0   0   1   4   0   0
    B         0   0 262   0   1   2   0   0   0   0
    C         0   0   0 552   0   0   0   0   1   0
    D         0   0   0   0  76   0   0   0   0   0
    F         0   0   0   0   0  12   0   0   0   3
    G         0   0   0   0   0   0  21   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   1   0   0   0   2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 0.476153 (all), 0.92787 (group)
Subtype Posterior Probability
03_AB 0
07_BC 4.7504e-43
08_BC 0
12_BF 0.00000000000000576671
14_BG 0
15_01B 0
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 5 / 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     9      0   1
   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: 3.88616 (all), 15.5529 (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: 7 / 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  56   0   1   0   0   0   2   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   9   0   0   3
    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: 14.4871 (all), 16.7339 (group)
Subtype Posterior Probability
03_AB 3.52845e-29
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 03_AB 12_BF 15_01B   B
   03_AB      0     0      0   0
   07_BC      0     0      0   0
   08_BC      0     0      0   0
   12_BF      0     9      0   0
   14_BG      0     0      0   0
   15_01B     0     0      3   0
   B          1     0      0 167

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vif (major) Outlierness: 1.99178 (all), 2.57676 (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: 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  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   3   0
    G         0   3   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   2   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vif (nested) Outlierness: 2.33301 (all), 3.4e38 (group)
Subtype Posterior Probability
03_AB 0.999874
12_BF 0
14_BG 0
15_01B 0
B 0.000126425

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: 1.43881 (all), 2.14075 (group)
Subtype Posterior Probability
01_AE 0.00000000000585192
A 4.55169e-21
B 1
C 2.78811e-30
D 0.0000000000000122717
F 0.000000019434
G 0.00000000000123178
H 0.000000000000105709
J 0.000000010552
K 0.0000000000000466596

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: 2.83897 (all), 3.20853 (group)
Subtype Posterior Probability
03_AB 0.000034031
07_BC 4.5076e-24
08_BC 1.96182e-44
12_BF 0.000183694
14_BG 5.55227e-17
15_01B 6.71915e-20
B 0.999782

Cross-Validation of Discriminant Models
Miss-Classification Rate: 12 / 300 at 10 Dimensional MDS
         Predicted
Objective 03_AB 07_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     0     0     0      0   0
   12_BF      0     0     6     0      0   2
   14_BG      0     0     0     0      0   0
   15_01B     0     0     0     1      2   0
   B          3     1     1     0      0 280

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (major) Outlierness: 1.23018 (all), 2.68183 (group)
Subtype Posterior Probability
01_AE 0
A 2.37861e-40
B 1
C 0
D 4.71891e-24
F 0
G 1.6453e-39
H 0
J 2.70536e-40
K 4.48416e-44

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         2  58   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  11   0   0   0   1
    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   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: 1.4839 (all), 3.4e38 (group)
Subtype Posterior Probability
03_AB 0.999988
07_BC 5.25709e-29
08_BC 5.40341e-42
12_BF 1.02091e-18
14_BG 3.2225e-34
15_01B 0
B 0.0000117734

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 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          1     0     0      0 158

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpu (major) Outlierness: 1.58352 (all), 2.29633 (group)
Subtype Posterior Probability
01_AE 6.45426e-37
A 8.13438e-30
B 1
C 2.4032e-29
D 0.000000000000179155
F 1.52249e-21
G 0.0000000000000186993
H 3.84022e-24
J 3.61818e-33
K 1.68112e-27

Cross-Validation of Discriminant Models
Miss-Classification Rate: 11 / 932 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J
    01_AE    45   1   0   0   0   0   0   0   0
    A         3  65   1   0   0   0   0   1   0
    B         0   0 321   0   0   0   0   0   0
    C         0   0   0 397   0   0   0   0   0
    D         0   0   1   0  53   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   2   0   0   0   0   0   4   0
    J         0   0   0   0   0   0   0   0   2
    K         0   0   1   0   0   0   1   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpu (nested) Outlierness: 2.68162 (all), 2.69091 (group)
Subtype Posterior Probability
03_AB 0.00000000000887306
08_BC 0.0000000000000870694
12_BF 0.260528
14_BG 0
15_01B 0
B 0.739472

Cross-Validation of Discriminant Models
Miss-Classification Rate: 14 / 340 at 10 Dimensional MDS
         Predicted
Objective 14_BG 15_01B   B
   03_AB      0      0   0
   08_BC      0      0   0
   12_BF      0      0  12
   14_BG      3      0   0
   15_01B     0      2   0
   B          0      0 321

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for nef (major) Outlierness: 1.08552 (all), 1.27987 (group)
Subtype Posterior Probability
01_AE 2.34431e-30
A 1.10769e-34
B 1
C 3.72627e-27
D 5.77911e-20
F 3.44819e-24
G 0
H 4.19639e-29
J 8.29201e-33
K 8.8671e-18

Cross-Validation of Discriminant Models
Miss-Classification Rate: 5 / 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         0   0   0 497   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: 2.19192 (all), 2.2216 (group)
Subtype Posterior Probability
03_AB 2.6933e-42
07_BC 5.44255e-31
08_BC 9.95774e-38
12_BF 2.0067e-18
14_BG 6.26801e-42
15_01B 8.632e-42
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: 1.26208 (all), 1.87131 (group)
Subtype Posterior Probability
01_AE 4.16186e-42
A 2.04342e-30
B 1
C 7.10838e-23
D 1.48485e-27
F 4.31492e-32
G 0
H 3.06473e-27
J 2.72505e-39
K 1.66431e-28

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: 3.08814 (all), 3.53189 (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: 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