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SLAC

SLAC usage summary as of Tue Aug 16 00:00:02 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (4286 days)92479 21.58 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 Tue Aug 16 00:00:14 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3386 days)104431 30.84 44.59243-787 488.423251-11276 182.27460-51470

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8547603 45.6
REV13414 12.8
TRN9310164 9.7
F815467 5.2
0100003929 3.8
0102322094 2.0
0120121584 1.5
0122121406 1.3
0102301270 1.2
0120321005 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 23.984473 80.9
0.05 0.9 19.115415 14.8
0.2 2.1 29.72137 2.0
0.25 3.1 31.9942 0.9
0.01 0.5 15.1530 0.5
0.5 6.0 43.1215 0.2
0.15 2.2 22.9182 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 Tue Aug 16 00:00:45 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3385 days)58372 17.24 20.71162-110 488.513231-11542 389.041110-54132

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8531083 53.2
REV5725 9.8
F813554 6.1
TRN933376 5.8
0100002345 4.0
0120121240 2.1
001101730 1.3
012212720 1.2
010232709 1.2
012032623 1.1
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.852765 90.4
100 4.4 22.11322 2.3
90 19.2 11.2901 1.5
20 7.2 36.0826 1.4
95 2.4 31.6784 1.3
10 5.8 31.7750 1.3
40 2.5 24.4145 0.2
25 7.8 34.7115 0.2
80 3.0 28.9111 0.2
30 9.8 20.693 0.2

TOGGLE

Toggle usage summary as of Tue Aug 16 00:00:52 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (4466 days)1095 0.25 47.56377-150 567.7435016-3789 3755.66196627-42841

Model Select.

ModelSelection usage summary as of Tue Aug 16 00:00:54 2022 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3386 days)103015 30.42 43.82223-656 523.503251-11935

Top 10 Models

ModelTimes selected% selected
HKY8524737 24.0
TRN9313124 12.7
F819029 8.8
0102324394 4.3
0120123621 3.5
0122123103 3.0
0102302487 2.4
0120322461 2.4
0122322439 2.4
0011012123 2.1

Protein Model Select.

ModelSelectionP usage summary as of Tue Aug 16 00:01:03 2022 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (5187 days)4241 0.82 46.17262-500 1067.064703-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F570 13.4
JTT (Jones,Taylor,Thornton)412 9.7
HIV (within host)+F412 9.7
BLOSUM62+F341 8.0
WAG (Whelan and Goldman)+F341 8.0
IAV (Influenza A virus)+F337 7.9
WAG (Whelan and Goldman)245 5.8
IAV (Influenza A virus)228 5.4
HIV (between hosts)+F180 4.2
BLOSUM62170 4.0

GARD

GARD usage summary as of Tue Aug 16 00:01:05 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days10 0.33 37.60 11.508-200 1671.202139427-2580 459.505225-3647
Lifetime (5739 days)76442 13.32 26.96182-300 2046.44111620-46625 1291.183861-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
064753 84.7
HKY855991 7.8
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
0-1027879 36.5
10-203043 4.0
20-302447 3.2
30-402278 3.0
40-501877 2.5
50-601980 2.6
60-701459 1.9
70-801325 1.7
80-901228 1.6
90-1001089 1.4
> 10031837 41.6
Number of breakpointsTimes found% found
023460 30.7
119349 25.3
212107 15.8
37046 9.2
44289 5.6
52949 3.9
61904 2.5
71419 1.9
8940 1.2
9764 1.0
≥ 102215 2.9

SBP

SBP usage summary as of Tue Aug 16 00:01:15 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days3 0.10 91.673936-200 1.3311-2 674.67915151-958
Lifetime (3386 days)21468 6.34 50.77252-656 21.7211-45015 699.18450-683633

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8515574 72.5
REV1315 6.1
010000565 2.6
F81503 2.3
TRN93502 2.3
0123455326 1.5
010232215 1.0
012012137 0.6
0112304567128 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-109272 43.2
10-20919 4.3
20-30808 3.8
30-40658 3.1
40-50528 2.5
50-60417 1.9
60-70364 1.7
70-80380 1.8
80-90295 1.4
90-100329 1.5
> 1007498 34.9

PARRIS

PARRIS usage summary as of Tue Aug 16 00:01:19 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (5494 days)14661 2.67 20.08153-75 491.593297-11903 424.601361-48648

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858319 56.7
F811080 7.4
REV1011 6.9
TRN93777 5.3
010000429 2.9
012012262 1.8
001101166 1.1
012212155 1.1
012032137 0.9
010230125 0.9
p-values rangeTimes found% found
0-0.12673 18.2
0.1-0.2518 3.5
0.2-0.3478 3.3
0.3-0.4373 2.5
0.4-0.5332 2.3
0.5-0.6393 2.7
0.6-0.7374 2.6
0.7-0.8361 2.5
0.8-0.9355 2.4
0.9-18804 60.1

GA Branch

GABranch usage summary as of Tue Aug 16 00:01:21 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days1 0.03111111-11563563563-563135135135-135
Lifetime (5487 days)11903 2.17 13.75123-30 522.333339-11628 5647.8415161-889396

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858630 72.5
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
24322 36.3
34028 33.8
42245 18.9
5783 6.6
6239 2.0
7119 1.0
840 0.3
928 0.2

CMS

CMS usage summary as of Tue Aug 16 00:01:23 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (4578 days)3439 0.75 33.10243-120 574.973527-1127620640.63404359-3262277

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10193 5.6
10-20152 4.4
20-30199 5.8
30-40234 6.8
40-50256 7.4
50-60184 5.4
60-70180 5.2
70-80133 3.9
80-90181 5.3
90-100112 3.3
> 1001615 47.0
Number of rate classesTimes found% found
10 0.0
22122 61.7
3753 21.9
4315 9.2
5139 4.0
656 1.6
717 0.5
82 0.1
91 0.0
≥ 1034 1.0

DEPS

DEPS usage summary as of Tue Aug 16 00:01:24 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (4457 days)3766 0.84 35.79313-100 1082.485569-11100 473.301412-31585

Subtyping

SCUEAL usage summary as of Tue Aug 16 00:01:25 2022 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days73767376.00 88.4040-500
Last 7 days73761053.71 88.4040-500
Last 30 days7376245.87 88.4040-500
Lifetime (4792 days)8680 1.81 91.9250-500

Top 10 Subtypes (out of 797859 sequences)

SubtypesTimes found% found
B314265 39.4
C153099 19.2
G52864 6.6
A147172 5.9
Complex33834 4.2
AE20841 2.6
D19948 2.5
CRF1412971 1.6
F112729 1.6
B,C recombinant9957 1.2

Coevolution

BGM usage summary as of Tue Aug 16 00:01:28 2022 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3386 days)8881 2.62 65.10300-1033 2.25 0.98 0.01-263 2866.47920-2900666

UCSD Viral Evolution Group 2004-2022