Launch prediction server Query precalculated results
Algorithms Prediction server Database query Output description Benchmark results

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 349 1867 963 A1DK A 03_AB Undecided
pol 1662 4671 2703 K 06_cpx Undecided
vif 4615 5194 522 G A A (Unambiguous Nested)
vpr 5133 5424 147 D D D (Unambiguous Nested)
5tat 5404 5615 185 D D D (Major agrees Nested with high confidence)
vpu 5648 5881 95 D D D (Major agrees Nested with high confidence)
env 5798 8378 1587 D 10_CD Undecided
nef 8379 9009 246 A 02_AG Undecided
ltr 8677 9229 256 H H Undecided

The sequence may not belong to the major group. Advised to be careful in interpreting the result.


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60229 CAA28011 gag 35 505 337 A 06_cpx Undecided


Detailed result for gag (major) Outlierness: 0.775435 (all), 1.06194 (group)
Subtype Posterior Probability
01_AE 0.00000000000234308
A 1
B 0
C 0
D 5.8294e-43
F 0
G 1.14647e-39
H 0.0000000000000109577
J 6.88979e-22
K 1.79124e-37

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: 0.704185 (all), 3.4e38 (group)
Subtype Posterior Probability
02_AG 0.000000000156841
03_AB 0.98754
04_cpx 0.000997493
06_cpx 0.0000000000000224855
09_cpx 0.00645287
11_cpx 0.0000000000010847
13_cpx 1.24363e-20
16_A2D 0.00000138331
A 0.00500819

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: 0.674502 (all), 114.566 (group)
Subtype Posterior Probability
01_AE 0
A 3.95543e-22
B 0
C 1.4013e-45
D 0
F 3.40003e-27
G 0
H 0.0000000310455
J 0.000000612312
K 0.999999

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: 21.4765 (all), 17.1025 (group)
Subtype Posterior Probability
04_cpx 0.0407645
06_cpx 0.959235
K 0.0000000000174757

Cross-Validation of Discriminant Models
Miss-Classification Rate: 5 / 10 at 10 Dimensional MDS
         Predicted
Objective 04_cpx 06_cpx K
   04_cpx      1      1 1
   06_cpx      1      3 1
   K           0      1 1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vif (major) Outlierness: 0.671193 (all), 2.80367 (group)
Subtype Posterior Probability
01_AE 0.00000000000004177
A 0.0447485
B 3.61881e-16
C 6.28321e-34
D 6.76619e-23
F 5.61009e-23
G 0.955251
H 0.000000000444463
J 0.000000332729
K 0.00000000000192706

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   3   0
    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: 0.411321 (all), 1.27686 (group)
Subtype Posterior Probability
02_AG 0.00165954
03_AB 1.49609e-16
04_cpx 3.7675e-19
06_cpx 0
09_cpx 0
11_cpx 2.92796e-27
13_cpx 1.4013e-45
14_BG 0.0000900316
16_A2D 0.00000000000417676
A 0.997502
G 0.000748403

Cross-Validation of Discriminant Models
Miss-Classification Rate: 11 / 166 at 10 Dimensional MDS
         Predicted
Objective 02_AG 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 14_BG 16_A2D  A  G
   02_AG     47      0      0      0      0      0     0      0  0  0
   03_AB      0      0      0      0      0      0     0      0  0  0
   04_cpx     0      3      0      0      0      0     0      0  0  0
   06_cpx     0      0      3      0      0      0     0      0  0  0
   09_cpx     0      0      0      4      0      0     0      0  0  0
   11_cpx     0      0      0      0      9      0     0      0  0  0
   13_cpx     0      0      0      0      0      3     0      0  0  0
   14_BG      0      0      0      0      0      0     1      0  0  2
   16_A2D     0      0      0      0      0      0     0      2  0  0
   A          2      0      0      0      0      0     1      4 67  0
   G          0      0      0      0      0      0     1      0  0 16

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpr (major) Outlierness: 0.713499 (all), 1.30342 (group)
Subtype Posterior Probability
01_AE 0.00000918805
A 0.0000967859
B 0.00349408
C 0.00000263669
D 0.996335
F 0.0000016058
G 0.000000000143208
H 0.0000602848
J 0.00000000937429
K 0.0000000000576285

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: 1.10107 (all), 1.12951 (group)
Subtype Posterior Probability
05_DF 6.30112e-16
10_CD 0.000000399118
16_A2D 0.00000000000000272971
D 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 4 / 52 at 10 Dimensional MDS
         Predicted
Objective 05_DF 10_CD 16_A2D  D
   05_DF      3     0      0  0
   10_CD      0     3      0  0
   16_A2D     0     0      1  1
   D          0     3      0 41

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (major) Outlierness: 0.954717 (all), 1.30176 (group)
Subtype Posterior Probability
01_AE 7.36542e-23
A 0.0000000000000868371
B 0.00000000000588407
C 5.66442e-24
D 1
F 2.69538e-16
G 8.106e-20
H 0.0000000000000602839
J 0.0000000000128102
K 0.000000000000632098

Cross-Validation of Discriminant Models
Miss-Classification Rate: 12 / 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  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   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: 1.00973 (all), 1.1304 (group)
Subtype Posterior Probability
05_DF 0.0214598
10_CD 3.72856e-27
16_A2D 0.00000000000000769708
D 0.97854

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 51 at 10 Dimensional MDS
         Predicted
Objective 05_DF 10_CD 16_A2D  D
   05_DF      1     0      0  2
   10_CD      0     2      0  0
   16_A2D     1     0      1  0
   D          4     0      0 40

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpu (major) Outlierness: 0.638164 (all), 1.34684 (group)
Subtype Posterior Probability
01_AE 0.0000000459344
A 0.000000917903
B 0.149305
C 0.00000000135146
D 0.848686
F 0.0020064
G 0.000000000966456
H 0.00000187685
J 3.56306e-17
K 4.89896e-18

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: 0.630164 (all), 0.965507 (group)
Subtype Posterior Probability
03_AB 0.00000695092
05_DF 0.00000667368
08_BC 1.32452e-19
10_CD 0.000000000000498006
12_BF 0.0135407
14_BG 6.95816e-32
15_01B 0.00000120681
16_A2D 1.79958e-17
B 0.0337244
D 0.95272

Cross-Validation of Discriminant Models
Miss-Classification Rate: 19 / 401 at 10 Dimensional MDS
         Predicted
Objective 05_DF 08_BC 10_CD 12_BF 14_BG 15_01B 16_A2D   B   D
   03_AB      0     0     0     0     0      0      0   0   0
   05_DF      2     0     0     0     0      0      0   0   0
   08_BC      0     0     0     0     0      0      0   0   0
   10_CD      0     2     1     0     0      0      0   0   0
   12_BF      0     0     0     1     0      0      0  11   0
   14_BG      0     0     0     0     3      0      0   0   0
   15_01B     0     0     0     0     0      1      0   0   1
   16_A2D     0     0     0     0     0      1      1   0   0
   B          0     0     0     1     0      0      0 320   0
   D          1     0     0     0     0      0      0   0  53

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (major) Outlierness: 0.663662 (all), 1.45436 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 8.75676e-40
C 0
D 1
F 0
G 0
H 1.1641e-30
J 0
K 2.53143e-31

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: 1.32501 (all), 7.33073 (group)
Subtype Posterior Probability
05_DF 0
10_CD 0.999998
16_A2D 0
D 0.00000205544

Cross-Validation of Discriminant Models
Miss-Classification Rate: 1 / 68 at 10 Dimensional MDS
         Predicted
Objective 05_DF 10_CD 16_A2D  D
   05_DF      3     0      0  0
   10_CD      0     3      0  0
   16_A2D     0     0      2  0
   D          0     1      0 59

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for nef (major) Outlierness: 0.797924 (all), 1.5159 (group)
Subtype Posterior Probability
01_AE 7.25545e-16
A 0.987765
B 0.0000000000000868905
C 0.0000000119293
D 0.00000000000000274719
F 0.00970553
G 0.00000000622432
H 0.00252894
J 0.0000000210979
K 0.0000000383989

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: 0.894305 (all), 1.22148 (group)
Subtype Posterior Probability
02_AG 0.821271
03_AB 0.11549
04_cpx 1.16032e-19
06_cpx 0.000000000000224922
09_cpx 0.0000233159
11_cpx 0.000000000000766349
13_cpx 0.0000000000179957
16_A2D 0.000000000528208
A 0.0632159

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 207 at 10 Dimensional MDS
         Predicted
Objective 02_AG 03_AB 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 16_A2D   A
   02_AG     69     0      0      0      0      0      0      0   0
   03_AB      0     0      0      0      0      0      0      0   0
   04_cpx     0     0      3      0      0      0      0      0   0
   06_cpx     0     0      0     11      0      0      0      0   0
   09_cpx     0     0      0      0      3      0      0      0   0
   11_cpx     0     0      0      0      0      5      1      0   0
   13_cpx     0     0      0      0      0      1      2      0   0
   16_A2D     0     0      0      0      0      0      0      2   0
   A          0     1      0      0      0      0      0      3 105

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for ltr (major) Outlierness: 1.45429 (all), 7.22006 (group)
Subtype Posterior Probability
01_AE 6.21411e-23
A 0.000172721
B 0.000000268531
C 1.33951e-21
D 0.000000000000138488
F 0.0000000732062
G 0.000000000154486
H 0.999827
J 2.65148e-17
K 0.000000000255915

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: -10.5182 (all), 8.37056 (group)
Subtype Posterior Probability
04_cpx 4.59477e-26
H 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 2 / 5 at 5 Dimensional MDS
         Predicted
Objective 04_cpx H
   04_cpx      2 0
   H           2 1

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