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SLAC

SLAC usage summary as of Wed May 24 00:00:01 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days108108.00 26.7073-264 343.6118931-3380 4.97 1.50 0.32- 75.16
Last 7 days314 44.86 38.80183-408 507.0432531-3738 13.82 2.78 0.32- 709.18
Last 30 days1646 54.87 38.97243-470 449.4132530-3786 11.59 3.50 0.19- 709.18
Lifetime (2376 days)75702 31.86 52.66253-684 482.853251-11903 23.12 6.54 0.16- 7571.98

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8539909 52.7
TRN9310517 13.9
REV8469 11.2
F813239 4.3
010232877 1.2
010230858 1.1
012212767 1.0
012012683 0.9
010000635 0.8
012232591 0.8
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 0.6 16.363119 83.4
0.05 0.6 14.59510 12.6
0.2 0.9 17.61088 1.4
0.25 2.4 25.8592 0.8
0.01 0.8 9.8489 0.6
0.5 4.4 54.2486 0.6
0.15 3.0 14.784 0.1
0.0024 0.0 2.345 0.1
0.3 0.2 20.543 0.1
0.0048 0.0 0.533 0.0

FEL

FEL usage summary as of Wed May 24 00:00:12 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days35 35.00 69.63414-264 624.31373100-3380 304.571645-1931
Last 7 days181 25.86 60.18293-408 523.0632585-3380 156.86635-1931
Last 30 days882 29.40 45.77303-443 425.3225130-3416 192.56734-10620
Lifetime (1476 days)90214 61.12 43.58243-787 472.113251-10798 140.87430-26278

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8540715 45.1
REV12255 13.6
TRN938735 9.7
F814289 4.8
0100003886 4.3
0102321930 2.1
0120121270 1.4
0122121223 1.4
0102301064 1.2
001101854 0.9
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.2 24.073084 81.0
0.05 0.9 18.713472 14.9
0.2 2.2 28.71674 1.9
0.25 3.3 32.8757 0.8
0.01 0.5 14.7452 0.5
0.5 5.6 44.5186 0.2
0.15 3.0 21.7125 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 May 24 00:00:24 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days16 16.00 11.38 7.504-41 307.7519688-1156 292.25 14.503-1826
Last 7 days127 18.14 19.25103-74 768.6541038-2207 360.43803-4374
Last 30 days448 14.93 22.61183-75 489.1130630-2207 322.50 143.503-4794
Lifetime (1475 days)50479 34.22 20.32152-110 476.783181-10798 358.911070-37794

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8526873 53.2
REV5269 10.4
TRN932866 5.7
F812764 5.5
0100002316 4.6
012012940 1.9
001101657 1.3
010232654 1.3
012212576 1.1
012032462 0.9
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.4 27.145538 90.2
100 4.2 22.41235 2.4
90 19.8 10.6870 1.7
20 7.0 36.8766 1.5
10 5.8 31.5713 1.4
95 2.6 26.1538 1.1
40 2.5 24.5144 0.3
80 3.4 27.194 0.2
30 10.2 20.689 0.2
25 2.8 34.171 0.1

TOGGLE

Toggle usage summary as of Wed May 24 00:00:30 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14888-8218218218-218221221221-221
Last 30 days10 0.33 47.80 30.508-10320518430-4385281 2038.50221-19272
Lifetime (2556 days)846 0.33 49.08 38.507-150 574.8833016-3789 3955.68 1977.5031-42841

Model Select.

ModelSelection usage summary as of Wed May 24 00:00:31 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days49 49.00 61.18574-264 580.5624955-3390
Last 7 days168 24.00 48.08413-404 475.7432538-3390
Last 30 days869 28.97 41.25253-500 513.05327 5.33-6503
Lifetime (1476 days)85993 58.26 41.05223-656 507.733251-11935

Top 10 Models

ModelTimes selected% selected
HKY8520862 24.3
TRN9311295 13.1
F817691 8.9
0102323917 4.6
0120122734 3.2
0122122534 2.9
0102302000 2.3
0011011831 2.1
0122321815 2.1
0120321761 2.0

Protein Model Select.

ModelSelectionP usage summary as of Wed May 24 00:00:39 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days3 3.00181818-18379379379-379
Last 7 days9 1.29 21.78184-43 365.44379153-551
Last 30 days31 1.03 36.65204-143 1182.61523153-4547
Lifetime (3277 days)3485 1.06 44.43242-499 623.244363-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F515 14.8
JTT (Jones,Taylor,Thornton)387 11.1
BLOSUM62+F286 8.2
WAG (Whelan and Goldman)+F281 8.1
WAG (Whelan and Goldman)232 6.7
HIV (within host)+F211 6.1
IAV (Influenza A virus)207 5.9
IAV (Influenza A virus)+F202 5.8
BLOSUM62149 4.3
LG (Le and Gascuel)142 4.1

GARD

GARD usage summary as of Wed May 24 00:00:40 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days11 11.00 83.911037-161 3533.181050264-10170 3677.09364571-15558
Last 7 days90 12.86 40.92214-296 1401.06 835.50114-11119 1605.94 280.5062-15558
Last 30 days296 9.87 36.11183-296 1822.42981114-11119 2305.93104354-40474
Lifetime (3829 days)70943 18.53 26.53182-300 2031.46111320-46625 1261.363671-174213

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
059254 83.5
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
0-1025427 35.8
10-202807 4.0
20-302263 3.2
30-402128 3.0
40-501724 2.4
50-601901 2.7
60-701347 1.9
70-801258 1.8
80-901165 1.6
90-1001032 1.5
> 10029891 42.1
Number of breakpointsTimes found% found
021312 30.0
117994 25.4
211207 15.8
36575 9.3
44002 5.6
52799 3.9
61806 2.5
71366 1.9
8914 1.3
9753 1.1
≥ 102215 3.1

SBP

SBP usage summary as of Wed May 24 00:00:50 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days2 2.00184184116-252 27.50 27.501-54276327631598-3928
Last 7 days50 7.14 53.80 22.504-408 14.1021-157 313.26 11.500-3928
Last 30 days120 4.00 89.79 39.503-471 8.9311-157 2656.02 107.500-34507
Lifetime (1476 days)19167 12.99 47.34252-656 21.5411-45015 469.63400-279793

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8513553 70.7
REV1310 6.8
010000565 2.9
TRN93497 2.6
F81489 2.6
010232214 1.1
0123455213 1.1
012012136 0.7
0112304567109 0.6
010230104 0.5
IC improvement rangeTimes found% found
0-108294 43.3
10-20845 4.4
20-30711 3.7
30-40581 3.0
40-50477 2.5
50-60376 2.0
60-70330 1.7
70-80347 1.8
80-90265 1.4
90-100282 1.5
> 1006659 34.7

PARRIS

PARRIS usage summary as of Wed May 24 00:00:53 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days3 3.001187-18 266.3320388-508 72.672823-167
Last 7 days26 3.71 14.4274-73 273.6922438-966 295.3810011-1616
Last 30 days108 3.60 17.41133-75 421.03 315.5030-1695 461.782456-3688
Lifetime (3584 days)13481 3.76 20.21153-75 484.853277-11903 416.721381-35284

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY857531 55.9
F811008 7.5
REV975 7.2
TRN93695 5.2
010000429 3.2
012012238 1.8
001101159 1.2
012212147 1.1
010230118 0.9
012032116 0.9
p-values rangeTimes found% found
0-0.12507 18.6
0.1-0.2473 3.5
0.2-0.3431 3.2
0.3-0.4328 2.4
0.4-0.5314 2.3
0.5-0.6363 2.7
0.6-0.7336 2.5
0.7-0.8329 2.4
0.8-0.9323 2.4
0.9-18077 59.9

GA Branch

GABranch usage summary as of Wed May 24 00:00:54 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days5 5.00 8.8097-1042124988-1156 2154.802072453-3901
Last 7 days30 4.29 10.6784-25 360.6323829-2170 2017.3371410-31880
Last 30 days67 2.23 13.75134-27 610.4523829-6503 5031.28104910-68415
Lifetime (3577 days)11258 3.15 13.73123-30 513.653299-11628 5339.5815081-636439

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858009 71.1
REV609 5.4
010000568 5.0
F81408 3.6
TRN93279 2.5
012012130 1.2
001101107 1.0
01221264 0.6
01001263 0.6
00001060 0.5
the number of dN/dS classes rangeTimes found% found
196 0.9
24116 36.6
33821 33.9
42105 18.7
5733 6.5
6223 2.0
7106 0.9
835 0.3
923 0.2

CMS

CMS usage summary as of Wed May 24 00:00:56 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29272711-43 438.50 438.50310-567386838682552-5184
Last 30 days26 0.87 35.50255-84 238.272478-56716815.466138559-104403
Lifetime (2668 days)2886 1.08 33.41243-120 531.893317-1079817501.41389959-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10178 6.2
10-20129 4.5
20-30177 6.1
30-40205 7.1
40-50224 7.8
50-60160 5.5
60-70162 5.6
70-80113 3.9
80-90161 5.6
90-100102 3.5
> 1001275 44.2
Number of rate classesTimes found% found
10 0.0
21841 63.8
3626 21.7
4235 8.1
592 3.2
644 1.5
713 0.5
81 0.0
90 0.0
≥ 1034 1.2

DEPS

DEPS usage summary as of Wed May 24 00:00:56 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00555-5723723723-723999-9
Last 7 days1 0.14555-5723723723-723999-9
Last 30 days8 0.27 12.38 13.503-21 1140.12 1467.5040-1695 139.50 135.509-333
Lifetime (2547 days)2549 1.00 30.92243-100 560.414479-6985 408.01972-31585

Subtyping

SCUEAL usage summary as of Wed May 24 00:00:57 2017 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days51205120.00 75.5730-500
Last 7 days5120731.43 75.5730-500
Last 30 days5120170.67 75.5730-500
Lifetime (2882 days)6424 2.23 82.9350-500

Top 10 Subtypes (out of 532732 sequences)

SubtypesTimes found% found
B208583 39.2
C96473 18.1
G40572 7.6
A133667 6.3
Complex21894 4.1
D16029 3.0
AE15041 2.8
CRF1411301 2.1
F18098 1.5
B,C recombinant6360 1.2

Coevolution

BGM usage summary as of Wed May 24 00:00:58 2017 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00333-3 1.33 1.33 1.33- 1.33000-0
Last 7 days9 1.29 38.1193-145 1.25 0.83 0.19-4 28.3380-157
Last 30 days25 0.8389203-860 2.66 1.33 0.03- 16.26 1402.04440-17954
Lifetime (1476 days)8349 5.66 64.96300-1033 2.25 0.97 0.01-263 2672.04960-2900666

UCSD Viral Evolution Group 2004-2017