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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
env 0 105 58 ? H 02_AG Undecided


Detailed result for env (major) Outlierness: 1.35884 (all), 20.7485 (group)
Subtype Posterior Probability
01_AE 0.00000000322573
A 0.480483
B 0.00000303553
C 0.0000115641
D 1.0575e-21
F 0.0000100794
G 0.0226885
H 0.492002
J 0.00479808
K 0.00000350311

Cross-Validation of Discriminant Models
Miss-Classification Rate: 216 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   G   H   J
    01_AE    68   0   2   0   0   0   0   0
    A         0  77   1   2   0   0   1   1
    B         1   0 409  40   3   1   0   0
    C         0   5 106 351   1   1   0   0
    D         0   0   8   3  49   0   0   0
    F         0   0   8   8   0   0   0   0
    G         0   2  10   6   0   5   0   0
    H         0   2   0   0   0   1   0   0
    J         0   0   0   0   0   0   0   0
    K         0   0   1   1   0   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 1.03148 (all), 1.01676 (group)
Subtype Posterior Probability
02_AG 0.731743
03_AB 0.0000000404901
04_cpx 0.000207381
06_cpx 0.00000000473287
09_cpx 0.000000713641
11_cpx 0.0650835
13_cpx 0.005643
14_BG 0.0000000170387
16_A2D 0.000000000000523971
A 0.196705
G 0.00000875911
H 0.000608369

Cross-Validation of Discriminant Models
Miss-Classification Rate: 99 / 196 at 10 Dimensional MDS
         Predicted
Objective 02_AG 04_cpx 06_cpx 09_cpx 11_cpx 14_BG  A  G  H
   02_AG     19      1      0      0      1     0 33  1  0
   03_AB      0      0      0      0      0     0  0  0  0
   04_cpx     2      0      0      1      0     0  0  0  0
   06_cpx     0      0      1      0      0     0  0  5  0
   09_cpx     0      1      0      0      1     0  1  1  0
   11_cpx     3      0      0      0      2     0  5  0  1
   13_cpx     0      0      0      0      0     0  3  0  0
   14_BG      0      0      0      0      0     0  0  3  0
   16_A2D     0      0      0      0      1     1  0  0  0
   A         13      0      1      1      3     1 58  2  3
   G          0      0      2      0      0     1  3 17  0
   H          0      0      0      0      1     0  1  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