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SLAC

SLAC usage summary as of Wed Jul 26 00:00:01 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days34 34.00 65.18 13.504-499 602.21 325.50106-2976 18.81 4.12 0.47- 241.96
Last 7 days479 68.43 39.38103-499 443.5526231-3411 10.95 1.74 0.27- 908.37
Last 30 days1464 48.80 41.85183-500 496.5132510-4249 10.53 2.63 0.27- 908.37
Lifetime (2439 days)78468 32.17 52.42253-684 483.493251-11903 22.71 6.44 0.16- 7571.98

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8541392 52.8
TRN9311174 14.2
REV8620 11.0
F813330 4.2
010232896 1.1
010230873 1.1
012212785 1.0
012012706 0.9
010000637 0.8
012232617 0.8
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 0.6 16.265543 83.5
0.05 0.6 14.59796 12.5
0.2 0.9 17.71103 1.4
0.25 2.4 25.3606 0.8
0.01 0.8 9.6503 0.6
0.5 4.4 54.5495 0.6
0.15 2.9 14.886 0.1
0.0024 0.0 2.345 0.1
0.3 0.2 20.444 0.1
0.0048 0.0 0.533 0.0

FEL

FEL usage summary as of Wed Jul 26 00:00:11 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days37 37.00 48.35114-321 828.62429106-2976 179.656314-1031
Last 7 days217 31.00 87.46453-466 621.9442922-3411 193.99717-2921
Last 30 days807 26.90 73.90453-500 509.8332510-3411 149.19843-2921
Lifetime (1539 days)91861 59.69 43.89243-787 471.973251-10798 140.52440-26278

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8541546 45.2
REV12445 13.5
TRN938905 9.7
F814401 4.8
0100003891 4.2
0102321940 2.1
0120121293 1.4
0122121236 1.3
0102301085 1.2
001101864 0.9
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.2 24.074292 80.9
0.05 0.9 19.013825 15.0
0.2 2.2 28.81728 1.9
0.25 3.3 32.6767 0.8
0.01 0.4 14.7469 0.5
0.5 5.6 44.5186 0.2
0.15 2.9 21.9128 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 Wed Jul 26 00:00:23 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days24 24.0023104-68 1070.79429106-2976 715.62 267.505-4379
Last 7 days126 18.00 23.29 10.503-71 652.7335622-3061 309.49 83.502-4379
Last 30 days339 11.30 26.60223-74 557.1438410-3061 270.861122-4379
Lifetime (1538 days)51450 33.45 20.45152-110 475.973171-10798 359.241080-38013

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8527431 53.3
REV5377 10.5
TRN932923 5.7
F812831 5.5
0100002317 4.5
012012958 1.9
001101666 1.3
010232659 1.3
012212585 1.1
012032480 0.9
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.4 27.246371 90.1
100 4.1 22.51262 2.5
90 19.6 10.9882 1.7
20 7.0 36.7769 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 Wed Jul 26 00:00:28 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days21 3.00392614-56 672.57650144-1135 3634.673167576-8536
Last 30 days57 1.90 38.58278-97 597.37464144-11353288257645-15246
Lifetime (2619 days)917 0.35 48.23387-150 571.1633616-3789 3910.38204331-42841

Model Select.

ModelSelection usage summary as of Wed Jul 26 00:00:29 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days28 28.00 50.32274-321 817.96 546.50106-3061
Last 7 days165 23.57 58.47293-466 855.5048041-3411
Last 30 days757 25.23 52.22303-466 683.1738210- 3999.67
Lifetime (1539 days)87616 56.93 41.23223-656 509.573251-11935

Top 10 Models

ModelTimes selected% selected
HKY8521140 24.1
TRN9311554 13.2
F817853 9.0
0102323953 4.5
0120122800 3.2
0122122571 2.9
0102302065 2.4
0122321861 2.1
0011011854 2.1
0120321819 2.1

Protein Model Select.

ModelSelectionP usage summary as of Wed Jul 26 00:00:37 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days1 1.00484848-48767767767-767
Last 7 days10 1.43 30.50256-88 708.90 726.50229-1149
Last 30 days17 0.57 35.24246-120 1017.2468666-4547
Lifetime (3340 days)3536 1.06 44.66242-499 633.244403-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F522 14.8
JTT (Jones,Taylor,Thornton)388 11.0
BLOSUM62+F293 8.3
WAG (Whelan and Goldman)+F283 8.0
WAG (Whelan and Goldman)234 6.6
IAV (Influenza A virus)+F213 6.0
HIV (within host)+F211 6.0
IAV (Influenza A virus)207 5.9
BLOSUM62157 4.4
LG (Le and Gascuel)144 4.1

GARD

GARD usage summary as of Wed Jul 26 00:00:38 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days10 10.00 64.60124-289 1332.50 1086.50318-2799 1791.10 1162.5036-5072
Last 7 days54 7.71 51.93 20.503-289 1169.28961208-9450 1246.35 436.5036-12010
Last 30 days187 6.23 45.26293-289 1830.40101193-11119 4314.1974036-272974
Lifetime (3892 days)71457 18.36 26.61182-300 2029.84111220-46625 1269.853681-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
059768 83.6
HKY855991 8.4
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
0-1025698 36.0
10-202827 4.0
20-302276 3.2
30-402136 3.0
40-501737 2.4
50-601903 2.7
60-701355 1.9
70-801261 1.8
80-901167 1.6
90-1001041 1.5
> 10030056 42.1
Number of breakpointsTimes found% found
021558 30.2
118114 25.3
211283 15.8
36603 9.2
44019 5.6
52806 3.9
61816 2.5
71374 1.9
8915 1.3
9754 1.1
≥ 102215 3.1

SBP

SBP usage summary as of Wed Jul 26 00:00:47 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days12 12.00 92.92 23.504-245 3.8311-281105 120.500-9093
Last 7 days60 8.57 157.38483-432 17.3041-107 1049.851670-9093
Last 30 days147 4.90 167.11813-479 22.4541-123 1084.276120-9093
Lifetime (1539 days)19442 12.63 48.51252-656 21.7911-45015 475.18410-279793

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8513803 71.0
REV1310 6.7
010000565 2.9
TRN93498 2.6
F81496 2.6
010232215 1.1
0123455214 1.1
012012137 0.7
0112304567110 0.6
010230104 0.5
IC improvement rangeTimes found% found
0-108458 43.5
10-20855 4.4
20-30718 3.7
30-40587 3.0
40-50482 2.5
50-60376 1.9
60-70333 1.7
70-80349 1.8
80-90266 1.4
90-100284 1.5
> 1006734 34.6

PARRIS

PARRIS usage summary as of Wed Jul 26 00:00:50 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days3 3.00 15.671010-27 239.67106106-507 288.6732366-477
Last 7 days10 1.43 30.30 24.506-57 345.10241106-933 205.60 160.5066-477
Last 30 days71 2.37 25.79223-65 463.9726952-1589 245.181817-1638
Lifetime (3647 days)13658 3.74 20.29153-75 483.133277-11903 414.791381-35284

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY857641 55.9
F811019 7.5
REV980 7.2
TRN93712 5.2
010000429 3.1
012012240 1.8
001101165 1.2
012212148 1.1
012032118 0.9
010230118 0.9
p-values rangeTimes found% found
0-0.12542 18.6
0.1-0.2482 3.5
0.2-0.3436 3.2
0.3-0.4334 2.4
0.4-0.5315 2.3
0.5-0.6366 2.7
0.6-0.7341 2.5
0.7-0.8333 2.4
0.8-0.9328 2.4
0.9-18181 59.9

GA Branch

GABranch usage summary as of Wed Jul 26 00:00:51 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days3 3.0015144-27 363.33382201-507 3329.33269213-7283
Last 7 days12 1.71 12.83 10.504-27 690.5838241-4518 1856.3348413-8027
Last 30 days30 1.00 13.97133-27 575.90 309.5041-4518 2755.60 647.503-27751
Lifetime (3640 days)11339 3.12 13.73123-30 513.563299-11628 5332.9815051-636439

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858088 71.3
REV610 5.4
010000568 5.0
F81408 3.6
TRN93279 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
196 0.8
24155 36.6
33843 33.9
42116 18.7
5740 6.5
6223 2.0
7108 1.0
835 0.3
923 0.2

CMS

CMS usage summary as of Wed Jul 26 00:00:52 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days3 0.43 50.335131-69 1385.33527218-341127732.33367834733-41681
Last 30 days22 0.73 37.14306-9775436431-3596143835090170-92818
Lifetime (2731 days)2933 1.07 33.50243-120 532.973327-1079817586.63390559-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10179 6.1
10-20131 4.5
20-30179 6.1
30-40209 7.1
40-50228 7.8
50-60163 5.6
60-70164 5.6
70-80116 4.0
80-90162 5.5
90-100104 3.5
> 1001298 44.3
Number of rate classesTimes found% found
10 0.0
21872 63.8
3636 21.7
4238 8.1
595 3.2
644 1.5
713 0.4
81 0.0
90 0.0
≥ 1034 1.2

DEPS

DEPS usage summary as of Wed Jul 26 00:00:53 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days3 3.00404626-481374767293-3062 970.33834194-1883
Last 7 days19 2.71 29.47269-88 600.53287124-3062 332.375423-1883
Last 30 days21 0.70 28.10249-88 561.5728766-3062 304.144923-1883
Lifetime (2610 days)2583 0.99 31.00243-100 567.664479-6985 410.77972-31585

Subtyping

SCUEAL usage summary as of Wed Jul 26 00:00:53 2017 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days53045304.00 77.9240-500
Last 7 days5304757.71 77.9240-500
Last 30 days5304176.80 77.9240-500
Lifetime (2945 days)6608 2.24 84.6150-500

Top 10 Subtypes (out of 559113 sequences)

SubtypesTimes found% found
B220669 39.5
C98193 17.6
G42256 7.6
A134153 6.1
Complex22958 4.1
D16377 2.9
AE15500 2.8
CRF1411505 2.1
F18482 1.5
B,C recombinant7417 1.3

Coevolution

BGM usage summary as of Wed Jul 26 00:00:55 2017 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days5 0.71 33.80373-57 1.84 1.10 0.09- 5.51 212.20730-576
Last 30 days52 1.73 56.04342-198 3.151 0.09- 85.40 329.54580-2906
Lifetime (1539 days)8427 5.48 64.94300-1033 2.26 0.97 0.01-263 2652.49960-2900666

UCSD Viral Evolution Group 2004-2017