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SLAC

SLAC usage summary as of Fri Apr 3 00:00:01 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3421 days)92479 27.03 53.07253-684 490.953251-11903 21.25 6.16 0.16- 7571.98

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8547511 51.4
TRN9313462 14.6
REV9543 10.3
F814265 4.6
0102301079 1.2
0120121076 1.2
0122121060 1.1
0102321010 1.1
012232856 0.9
012032760 0.8
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 0.6 16.277137 83.4
0.05 0.5 14.111486 12.4
0.2 0.9 18.41381 1.5
0.25 2.2 24.8776 0.8
0.5 4.3 55.2659 0.7
0.01 0.8 9.6540 0.6
0.15 2.2 15.2115 0.1
0.3 0.2 18.151 0.1
0.0024 0.0 2.345 0.0
0.0048 0.0 0.533 0.0

FEL

FEL usage summary as of Fri Apr 3 00:00:14 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days15 15.00 126.4777-483 489.27419419-759 256.93109-1163
Last 7 days63 9.00 88.51123-483 645.8342475-3972 1773.102982-18639
Last 30 days179 5.97 72.30263-483 935.3444653-9744 4661.4124552-45868
Lifetime (2521 days)102880 40.81 44.45243-787 485.323251-11276 173.18460-51470

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8546644 45.3
REV13270 12.9
TRN9310088 9.8
F815313 5.2
0100003928 3.8
0102322083 2.0
0120121582 1.5
0122121391 1.4
0102301265 1.2
012032998 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.083176 80.8
0.05 0.9 19.115237 14.8
0.2 2.1 29.82122 2.1
0.25 3.1 31.9928 0.9
0.01 0.4 14.7520 0.5
0.5 5.9 43.2214 0.2
0.15 2.5 23.4162 0.2
0.0024 0.0 7.0102 0.1
0.3 1.2 23.364 0.1
0.06 0.3 22.560 0.1

REL

REL usage summary as of Fri Apr 3 00:00:27 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days18 18.00777-7419419419-419 15.28156-29
Last 7 days69 9.86 6.1943-21 436.4841952-1273 90.97290-1257
Last 30 days167 5.57 19.83123-71 637.2041952-9744 884.632020-29079
Lifetime (2520 days)57417 22.78 20.67162-110 486.683231-10798 391.141110-54132

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8530498 53.1
REV5686 9.9
F813457 6.0
TRN933344 5.8
0100002341 4.1
0120121205 2.1
001101730 1.3
012212704 1.2
010232698 1.2
012032614 1.1
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.851929 90.4
100 4.4 22.21312 2.3
90 19.2 11.2901 1.6
20 7.2 35.9821 1.4
10 5.8 31.9747 1.3
95 2.2 31.0723 1.3
40 2.5 24.4145 0.3
80 3.0 28.0109 0.2
25 8.6 34.1104 0.2
30 10.0 20.291 0.2

TOGGLE

Toggle usage summary as of Fri Apr 3 00:00:34 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3601 days)1081 0.30 47.60377-150 571.6435016-3789 3781.73196831-42841

Model Select.

ModelSelection usage summary as of Fri Apr 3 00:00:36 2020 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days5 5.00 365.404627-483 629.80716419-759
Last 7 days32 4.57 172.72 36.503-483 889.51514 186.33-3972
Last 30 days134 4.47 88.07363-483 855.04 296.5057-9744
Lifetime (2521 days)101317 40.19 43.81223-656 520.663251-11935

Top 10 Models

ModelTimes selected% selected
HKY8524329 24.0
TRN9313025 12.9
F818750 8.6
0102324337 4.3
0120123554 3.5
0122123050 3.0
0102302474 2.4
0120322413 2.4
0122322408 2.4
0011012098 2.1

Protein Model Select.

ModelSelectionP usage summary as of Fri Apr 3 00:00:45 2020 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days9 0.30 32.44323-52 5658.569626621-9744
Lifetime (4322 days)3900 0.90 46.49252-500 663.48 445.503-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F564 14.5
JTT (Jones,Taylor,Thornton)407 10.4
BLOSUM62+F326 8.4
WAG (Whelan and Goldman)+F323 8.3
HIV (within host)+F259 6.6
WAG (Whelan and Goldman)244 6.3
IAV (Influenza A virus)+F241 6.2
IAV (Influenza A virus)228 5.8
BLOSUM62169 4.3
LG (Le and Gascuel)166 4.3

GARD

GARD usage summary as of Fri Apr 3 00:00:47 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days6 0.86 116.17 74.5012-262386736481206-9342 3019.17 4112.50326-4649
Last 30 days33 1.1055234-262 5080.271539171-291033012976294-29966
Lifetime (4874 days)75487 15.49 26.92182-300 2039.86111620-46625 1290.433851-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
063798 84.5
HKY855991 7.9
010000860 1.1
REV830 1.1
TRN93558 0.7
F81520 0.7
010232226 0.3
012212218 0.3
010230182 0.2
012232144 0.2
delta AIC rangeTimes found% found
0-1027437 36.3
10-203008 4.0
20-302432 3.2
30-402260 3.0
40-501855 2.5
50-601965 2.6
60-701439 1.9
70-801319 1.7
80-901219 1.6
90-1001084 1.4
> 10031469 41.7
Number of breakpointsTimes found% found
023092 30.6
119098 25.3
211963 15.8
36960 9.2
44247 5.6
52916 3.9
61886 2.5
71414 1.9
8935 1.2
9761 1.0
≥ 102215 2.9

SBP

SBP usage summary as of Fri Apr 3 00:00:57 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days4 0.57 119.253119-396 3.25 2.501-7 1491.75 442.50161-4921
Last 30 days32 1.07 64.193311-396 5.0311-78 1951.4749534-28626
Lifetime (2521 days)20961 8.31 49.96252-656 21.7711-45015 601.24430-683633

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8515189 72.5
REV1315 6.3
010000565 2.7
F81503 2.4
TRN93502 2.4
0123455254 1.2
010232215 1.0
012012137 0.7
0112304567120 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-109076 43.3
10-20903 4.3
20-30799 3.8
30-40648 3.1
40-50512 2.4
50-60410 2.0
60-70360 1.7
70-80376 1.8
80-90286 1.4
90-100320 1.5
> 1007271 34.7

PARRIS

PARRIS usage summary as of Fri Apr 3 00:01:00 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00777-7419419419-419202020-20
Last 7 days5 0.71 5.6064-7 1371.20514419-3972 25.802012-56
Last 30 days10 0.33 11.2064-33 1608.80576182-3984881 63.5012-4683
Lifetime (4629 days)14484 3.13 20.12153-75 488.423297-11903 426.461371-48648

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858184 56.5
F811071 7.4
REV1008 7.0
TRN93766 5.3
010000429 3.0
012012262 1.8
001101166 1.1
012212155 1.1
012032137 0.9
010230125 0.9
p-values rangeTimes found% found
0-0.12649 18.3
0.1-0.2514 3.5
0.2-0.3467 3.2
0.3-0.4369 2.5
0.4-0.5331 2.3
0.5-0.6391 2.7
0.6-0.7370 2.6
0.7-0.8359 2.5
0.8-0.9354 2.4
0.9-18680 59.9

GA Branch

GABranch usage summary as of Fri Apr 3 00:01:02 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.2915156-24 2235.50 2235.50514-39577191371913536-143290
Last 30 days4 0.13 11.2585-24 1422.25 656.50419-395736145.25 552.50186-143290
Lifetime (4622 days)11762 2.54 13.74123-30 520.443319-11628 5665.76 1516.501-889396

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858489 72.2
REV614 5.2
010000568 4.8
F81415 3.5
TRN93285 2.4
012012131 1.1
001101107 0.9
01221264 0.5
01001263 0.5
00001060 0.5
the number of dN/dS classes rangeTimes found% found
199 0.8
24299 36.5
33973 33.8
42201 18.7
5774 6.6
6234 2.0
7118 1.0
839 0.3
925 0.2

CMS

CMS usage summary as of Fri Apr 3 00:01:04 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29 49.50 49.5024-7522082208459-395739425.5039425.504708-74143
Last 30 days7 0.23 32.57247-75131956285-395719377.4372101960-74143
Lifetime (3713 days)3250 0.88 33.73243-120 569.023437-1127621126.57404459-3262277

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10190 5.8
10-20151 4.6
20-30190 5.8
30-40221 6.8
40-50246 7.6
50-60179 5.5
60-70174 5.4
70-80129 4.0
80-90175 5.4
90-100111 3.4
> 1001484 45.7
Number of rate classesTimes found% found
10 0.0
22044 62.9
3712 21.9
4276 8.5
5116 3.6
650 1.5
715 0.5
82 0.1
91 0.0
≥ 1034 1.0

DEPS

DEPS usage summary as of Fri Apr 3 00:01:05 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days12 0.40455220-52 8326.33 9647.50555-9744 242.17 170.5088-455
Lifetime (3592 days)3427 0.95 35.29303-100 679.815089-11100 500.741412-31585

Subtyping

SCUEAL usage summary as of Fri Apr 3 00:01:07 2020 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days65876587.00 83.9540-500
Last 7 days6587941.00 83.9540-500
Last 30 days6587219.57 83.9540-500
Lifetime (3927 days)7891 2.01 88.5650-500

Top 10 Subtypes (out of 698835 sequences)

SubtypesTimes found% found
B263256 37.7
C140163 20.1
G46494 6.7
A142287 6.1
Complex28631 4.1
AE19954 2.9
D19014 2.7
CRF1411765 1.7
F110659 1.5
B,C recombinant9244 1.3

Coevolution

BGM usage summary as of Fri Apr 3 00:01:09 2020 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (2521 days)8881 3.52 65.10300-1033 2.25 0.98 0.01-263 2866.47920-2900666

UCSD Viral Evolution Group 2004-2020