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SLAC

SLAC usage summary as of Mon Aug 21 00:00:02 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days68 68.00 13.81103-45 293.32 208.5031-1509 2.31 1.53 0.50- 6.87
Last 7 days741105.86 62.75193-489 247.881014-3551 5.16 1.67 0.24- 230.83
Last 30 days1967 65.57 51.94183-499 422.082224-6267 7.95 2.19 0.22- 908.37
Lifetime (2465 days)80220 32.54 52.37253-684 482.003251-11903 22.35 6.36 0.16- 7571.98

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8542242 52.7
TRN9311655 14.5
REV8809 11.0
F813408 4.2
010232901 1.1
010230880 1.1
012212787 1.0
012012712 0.9
010000640 0.8
012232623 0.8
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 0.6 16.067137 83.7
0.05 0.6 14.69925 12.4
0.2 0.9 17.71117 1.4
0.25 2.3 25.4612 0.8
0.01 0.8 9.6505 0.6
0.5 4.4 54.6500 0.6
0.15 2.9 14.886 0.1
0.0024 0.0 2.345 0.1
0.3 0.2 20.045 0.1
0.0048 0.0 0.533 0.0

FEL

FEL usage summary as of Mon Aug 21 00:00:12 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days5 5.00 50.604521-120 275.80261207-325 79.205534-193
Last 7 days155 22.14 66.22284-430 457.0826523-2924 139.69752-1795
Last 30 days886 29.53 66.05263-494 529.74 310.5020-6267 180.17692-7245
Lifetime (1565 days)92595 59.17 44.01243-787 472.303251-10798 140.77440-26278

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8541923 45.3
REV12520 13.5
TRN938978 9.7
F814442 4.8
0100003892 4.2
0102321953 2.1
0120121300 1.4
0122121246 1.3
0102301095 1.2
001101864 0.9
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.2 24.174876 80.9
0.05 0.9 19.013959 15.1
0.2 2.2 28.71735 1.9
0.25 3.3 32.7772 0.8
0.01 0.4 14.6472 0.5
0.5 5.6 44.5186 0.2
0.15 2.9 21.7129 0.1
0.0024 0.0 7.0102 0.1
0.3 1.2 22.363 0.1
0.0004 0.0 6.629 0.0

REL

REL usage summary as of Mon Aug 21 00:00:23 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days8 8.00 26.622121-65261261261-261238 173.5057-699
Last 7 days84 12.00 23.57213-74 409.6026137-2886 199.711413-796
Last 30 days449 14.97 20.09153-75 470.5726122-3061 244.27832-6918
Lifetime (1564 days)51801 33.12 20.44152-110 475.613161-10798 358.381080-38013

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8527618 53.3
REV5402 10.4
TRN932942 5.7
F812867 5.5
0100002319 4.5
012012964 1.9
001101666 1.3
010232661 1.3
012212616 1.2
012032486 0.9
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.4 27.346714 90.2
100 4.1 22.61265 2.4
90 19.6 10.9882 1.7
20 7.1 36.6772 1.5
10 5.8 31.7717 1.4
95 2.3 27.9611 1.2
40 2.5 24.5144 0.3
80 3.2 27.199 0.2
30 10.2 20.689 0.2
25 2.6 36.276 0.1

TOGGLE

Toggle usage summary as of Mon Aug 21 00:00:29 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days4 0.5747 40.5018-89 198.50202156-234 6589.752928380-20123
Last 30 days48 1.60 51.444614-108 546.2946452-1135 4343.46 2879.50128-20123
Lifetime (2645 days)959 0.36 48.55397-150 570.5534516-3789 3942.33207731-42841

Model Select.

ModelSelection usage summary as of Mon Aug 21 00:00:30 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days21 21.00 72.624521-185 413.10325261-884
Last 7 days174 24.86 47.01 25.503-330 526.3432523-3551
Last 30 days823 27.43 49.57213-494 641.0732511-6267
Lifetime (1565 days)88352 56.45 41.26223-656 510.683251-11935

Top 10 Models

ModelTimes selected% selected
HKY8521293 24.1
TRN9311647 13.2
F817930 9.0
0102323973 4.5
0120122818 3.2
0122122584 2.9
0102302100 2.4
0122321881 2.1
0011011860 2.1
0120321855 2.1

Protein Model Select.

ModelSelectionP usage summary as of Mon Aug 21 00:00:37 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days7 1.00 44.57226-93 1698.57824107-5742
Last 30 days30 1.00 35.27286-133 818.83 478.50107-5742
Lifetime (3366 days)3564 1.06 44.59242-499 634.724403-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F529 14.8
JTT (Jones,Taylor,Thornton)389 10.9
BLOSUM62+F295 8.3
WAG (Whelan and Goldman)+F290 8.1
WAG (Whelan and Goldman)234 6.6
IAV (Influenza A virus)+F214 6.0
HIV (within host)+F212 5.9
IAV (Influenza A virus)207 5.8
BLOSUM62157 4.4
LG (Le and Gascuel)145 4.1

GARD

GARD usage summary as of Mon Aug 21 00:00:39 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days86 12.29 30.41183-291 2773.31 1406.50111-10653 1746.5964864-19014
Last 30 days370 12.33 34.18153-291 1785.37 952.50111-11225 1145.7541836-19014
Lifetime (3918 days)71802 18.33 26.63182-300 2028.76111020-46625 1268.983691-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
060113 83.7
HKY855991 8.3
010000860 1.2
REV830 1.2
TRN93558 0.8
F81520 0.7
010232226 0.3
012212218 0.3
010230182 0.3
012232144 0.2
delta AIC rangeTimes found% found
0-1025871 36.0
10-202856 4.0
20-302304 3.2
30-402144 3.0
40-501747 2.4
50-601912 2.7
60-701357 1.9
70-801263 1.8
80-901170 1.6
90-1001042 1.5
> 10030136 42.0
Number of breakpointsTimes found% found
021694 30.2
118219 25.4
211341 15.8
36624 9.2
44033 5.6
52808 3.9
61818 2.5
71376 1.9
8919 1.3
9755 1.1
≥ 102215 3.1

SBP

SBP usage summary as of Mon Aug 21 00:00:48 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days38 5.43 51.84 17.503-291 8.95 1.501-59 374.76650-1978
Last 30 days173 5.77 66.36113-494 23.8231-805 556.26360-16478
Lifetime (1565 days)19584 12.51 48.46252-656 21.8311-45015 474.77400-279793

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8513929 71.1
REV1311 6.7
010000565 2.9
TRN93498 2.5
F81497 2.5
0123455216 1.1
010232215 1.1
012012137 0.7
0112304567111 0.6
010230104 0.5
IC improvement rangeTimes found% found
0-108486 43.3
10-20872 4.5
20-30732 3.7
30-40593 3.0
40-50483 2.5
50-60384 2.0
60-70338 1.7
70-80352 1.8
80-90274 1.4
90-100285 1.5
> 1006785 34.6

PARRIS

PARRIS usage summary as of Mon Aug 21 00:00:50 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days5 5.00212121-21261261261-261135132129-147
Last 7 days13 1.86 17.85216-25 309.6226137-1253 473.381306-4919
Last 30 days61 2.03 18.10173-75 296.9323837-1253 189.16633-4919
Lifetime (3673 days)13713 3.73 20.28153-75 482.353277-11903 413.871381-35284

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY857672 55.9
F811027 7.5
REV983 7.2
TRN93713 5.2
010000429 3.1
012012242 1.8
001101165 1.2
012212150 1.1
012032120 0.9
010230118 0.9
p-values rangeTimes found% found
0-0.12549 18.6
0.1-0.2483 3.5
0.2-0.3438 3.2
0.3-0.4337 2.5
0.4-0.5316 2.3
0.5-0.6368 2.7
0.6-0.7345 2.5
0.7-0.8336 2.5
0.8-0.9329 2.4
0.9-18212 59.9

GA Branch

GABranch usage summary as of Mon Aug 21 00:00:52 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days6 0.861084-19 714.83 437.50235-1691 5068.83117317-18000
Last 30 days56 1.87 14.20143-28 426.2523583-4518 3443.2715593-30487
Lifetime (3666 days)11387 3.11 13.74123-30 512.893299-11628 5326.2815061-636439

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858135 71.4
REV610 5.4
010000568 5.0
F81408 3.6
TRN93280 2.5
012012131 1.2
001101107 0.9
01221264 0.6
01001263 0.6
00001060 0.5
the number of dN/dS classes rangeTimes found% found
197 0.9
24172 36.6
33859 33.9
42125 18.7
5745 6.5
6223 2.0
7108 0.9
835 0.3
923 0.2

CMS

CMS usage summary as of Mon Aug 21 00:00:53 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days4 0.57 40.50 34.504-89 402.25214174-100752368.2526059380-156975
Last 30 days27 0.90 43.56253-120 394.8932583-100713374.743837159-156975
Lifetime (2757 days)2960 1.07 33.59243-120 531.71 331.507-1079817548.21390459-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10182 6.1
10-20135 4.6
20-30180 6.1
30-40209 7.1
40-50230 7.8
50-60164 5.5
60-70165 5.6
70-80122 4.1
80-90164 5.5
90-100104 3.5
> 1001305 44.1
Number of rate classesTimes found% found
10 0.0
21894 64.0
3637 21.5
4241 8.1
595 3.2
644 1.5
714 0.5
81 0.0
90 0.0
≥ 1034 1.1

DEPS

DEPS usage summary as of Mon Aug 21 00:00:54 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days3 0.43 53.337118-71 360.67193193-696 204.67181172-261
Last 30 days29 0.97 25.14243-71 453.17289124-3062 202.2110711-1883
Lifetime (2636 days)2599 0.99 30.98243-100 566.534469-6985 408.98982-31585

Subtyping

SCUEAL usage summary as of Mon Aug 21 00:00:54 2017 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days53895389.00 77.8140-500
Last 7 days5389769.86 77.8140-500
Last 30 days5389179.63 77.8140-500
Lifetime (2971 days)6693 2.25 84.4450-500

Top 10 Subtypes (out of 565138 sequences)

SubtypesTimes found% found
B222973 39.5
C98663 17.5
G42318 7.5
A134243 6.1
Complex23227 4.1
D16459 2.9
AE15805 2.8
CRF1411506 2.0
F18525 1.5
B,C recombinant7457 1.3

Coevolution

BGM usage summary as of Mon Aug 21 00:00:56 2017 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days11 1.57 52.45322-175 3.48 2.03 0.03- 17.97 642.09320-5318
Last 30 days56 1.87 42.77272-215 2.52 1.21 0.03- 44.40 492.41 36.500-7899
Lifetime (1565 days)8478 5.42 64.81300-1033 2.26 0.97 0.01-263 2639.66950-2900666

UCSD Viral Evolution Group 2004-2017