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SLAC

SLAC usage summary as of Mon Jun 18 00:00:01 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00131131131-131533533533-533 48.48 48.48 48.48- 48.48
Last 7 days68 9.71 31.46213-139 487.5435091-2332 5.20 2.56 0.23- 48.48
Last 30 days451 15.03 38.29273-412 693.7532510-9793 10.62 3.61 0.23- 985.61
Lifetime (2766 days)88001 31.82 51.92253-684 488.453251-11903 21.42 6.22 0.16- 7571.98

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8545520 51.7
TRN9313111 14.9
REV9311 10.6
F813901 4.4
010230994 1.1
010232982 1.1
012212935 1.1
012012857 1.0
012232753 0.9
010000660 0.7
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 0.6 16.273770 83.8
0.05 0.5 14.510639 12.1
0.2 0.9 17.31291 1.5
0.25 2.3 25.7727 0.8
0.5 4.4 55.7616 0.7
0.01 0.8 9.4522 0.6
0.15 2.8 15.392 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 Jun 18 00:00:12 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days83 11.86 31.11163-134 559.0745895-2022 62.63353-667
Last 30 days298 9.93 41.45203-476 671.37 404.5066-3999 104.94 34.503-1482
Lifetime (1866 days)98063 52.55 44.25243-787 479.503251-11276 140.84440-26278

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8544164 45.0
REV12892 13.1
TRN939661 9.9
F814833 4.9
0100003918 4.0
0102322032 2.1
0120121429 1.5
0122121327 1.4
0102301201 1.2
012032942 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.279419 81.0
0.05 0.9 19.314554 14.8
0.2 2.1 29.01953 2.0
0.25 3.2 33.4850 0.9
0.01 0.4 14.4486 0.5
0.5 5.4 43.3196 0.2
0.15 2.8 22.4136 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 Jun 18 00:00:24 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days31 4.43 15.87153-38 590.90428109-1664 166.19491-2286
Last 30 days130 4.33 14.92113-59 715.82 437.5066-3551 180.61 53.501-2286
Lifetime (1865 days)54693 29.33 20.60162-110 481.663191-10798 363.381080-39109

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8528958 52.9
REV5579 10.2
TRN933206 5.9
F813117 5.7
0100002329 4.3
0120121072 2.0
001101720 1.3
010232683 1.2
012212667 1.2
012032559 1.0
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.749408 90.3
100 4.2 22.61284 2.3
90 19.4 11.1890 1.6
20 7.3 36.2808 1.5
10 5.8 32.0729 1.3
95 2.3 28.0642 1.2
40 2.5 24.5144 0.3
80 3.0 28.5107 0.2
30 10.2 20.689 0.2
25 2.5 38.880 0.1

TOGGLE

Toggle usage summary as of Mon Jun 18 00:00:30 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (2946 days)1041 0.35 48.35397-150 570.3334616-3789 3832.75201431-42841

Model Select.

ModelSelection usage summary as of Mon Jun 18 00:00:31 2018 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days72 10.29 21.54153-134 510.64375109-2022
Last 30 days260 8.67 31.49153-476 520.82 324.5066-3787
Lifetime (1866 days)95213 51.03 41.54223-656 515.633251-11935

Top 10 Models

ModelTimes selected% selected
HKY8522868 24.0
TRN9312572 13.2
F818373 8.8
0102324198 4.4
0120123123 3.3
0122122823 3.0
0102302247 2.4
0120322179 2.3
0122322133 2.2
0011011999 2.1

Protein Model Select.

ModelSelectionP usage summary as of Mon Jun 18 00:00:39 2018 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days11 1.57 69.824410-287 1805.45110112-4516
Last 30 days26 0.87 47.04379-287 1442.27 974.5012-4516
Lifetime (3667 days)3760 1.03 45.86252-499 652.684443-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F549 14.6
JTT (Jones,Taylor,Thornton)399 10.6
BLOSUM62+F313 8.3
WAG (Whelan and Goldman)+F308 8.2
WAG (Whelan and Goldman)241 6.4
IAV (Influenza A virus)+F235 6.2
HIV (within host)+F232 6.2
IAV (Influenza A virus)216 5.7
BLOSUM62165 4.4
LG (Le and Gascuel)159 4.2

GARD

GARD usage summary as of Mon Jun 18 00:00:40 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days9 1.29 76.674210-299 3045.561262459-6996 2688.33334899-6308
Last 30 days87 2.90 33.25133-299 2039.20772198-10653 1543.4022236-9991
Lifetime (4219 days)73815 17.50 26.83182-300 2029.89111020-46625 1270.273741-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
062126 84.2
HKY855991 8.1
010000860 1.2
REV830 1.1
TRN93558 0.8
F81520 0.7
010232226 0.3
012212218 0.3
010230182 0.2
012232144 0.2
delta AIC rangeTimes found% found
0-1026798 36.3
10-202940 4.0
20-302371 3.2
30-402212 3.0
40-501816 2.5
50-601940 2.6
60-701399 1.9
70-801297 1.8
80-901193 1.6
90-1001068 1.4
> 10030781 41.7
Number of breakpointsTimes found% found
022514 30.5
118720 25.4
211693 15.8
36769 9.2
44113 5.6
52846 3.9
61849 2.5
71403 1.9
8932 1.3
9761 1.0
≥ 102215 3.0

SBP

SBP usage summary as of Mon Jun 18 00:00:49 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00333333333-333444444-44855085508550-8550
Last 7 days18 2.57 76.893014-340 5.3911-44 1061.944910-8550
Last 30 days35 1.17 108.63419-427 10.2311-64 1986.602301-15878
Lifetime (1866 days)20228 10.84 48.64242-656 21.7211-45015 475.16410-279793

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8514524 71.8
REV1311 6.5
010000565 2.8
TRN93501 2.5
F81500 2.5
0123455224 1.1
010232215 1.1
012012137 0.7
0112304567115 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-108735 43.2
10-20889 4.4
20-30767 3.8
30-40620 3.1
40-50504 2.5
50-60403 2.0
60-70351 1.7
70-80372 1.8
80-90279 1.4
90-100300 1.5
> 1007008 34.6

PARRIS

PARRIS usage summary as of Mon Jun 18 00:00:52 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days3 0.43 5.6744-9 614.67649546-6494997-131
Last 30 days13 0.43 18.15134-37 295.926666-781 266.541317-709
Lifetime (3974 days)14164 3.56 20.19153-75 484.153287-11903 414.731361-35284

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY857992 56.4
F811054 7.4
REV996 7.0
TRN93737 5.2
010000429 3.0
012012250 1.8
001101166 1.2
012212153 1.1
012032127 0.9
010230119 0.8
p-values rangeTimes found% found
0-0.12601 18.4
0.1-0.2503 3.6
0.2-0.3458 3.2
0.3-0.4361 2.5
0.4-0.5325 2.3
0.5-0.6386 2.7
0.6-0.7363 2.6
0.7-0.8351 2.5
0.8-0.9346 2.4
0.9-18470 59.8

GA Branch

GABranch usage summary as of Mon Jun 18 00:00:53 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29994-14 538.50 538.50428-649322532256-6444
Last 30 days22 0.7314114-30 769.7732258-3999 3266.3618666-9931
Lifetime (3967 days)11607 2.93 13.73123-30 515.233299-11628 5292.5815071-636439

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858340 71.9
REV613 5.3
010000568 4.9
F81414 3.6
TRN93281 2.4
012012131 1.1
001101107 0.9
01221264 0.6
01001263 0.5
00001060 0.5
the number of dN/dS classes rangeTimes found% found
199 0.9
24252 36.6
33925 33.8
42175 18.7
5759 6.5
6228 2.0
7111 1.0
835 0.3
923 0.2

CMS

CMS usage summary as of Mon Jun 18 00:00:54 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29 15.50 15.5014-17 966.50 966.50428-150521161211617174-35148
Last 30 days6 0.20 20.671914-36630 544.50192-150512040.33 4468.501256-35148
Lifetime (3058 days)3085 1.01 33.82243-120 536.933357-1127617787.87391859-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10183 5.9
10-20142 4.6
20-30186 6.0
30-40212 6.9
40-50239 7.7
50-60174 5.6
60-70170 5.5
70-80126 4.1
80-90172 5.6
90-100107 3.5
> 1001374 44.5
Number of rate classesTimes found% found
10 0.0
21964 63.7
3671 21.8
4254 8.2
5101 3.3
645 1.5
714 0.5
82 0.1
90 0.0
≥ 1034 1.1

DEPS

DEPS usage summary as of Mon Jun 18 00:00:55 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29 23.50 23.5010-371178117824-233230430426-582
Last 30 days8 0.27 19.88109-37 1463.50233212-2332 180.382721-582
Lifetime (2937 days)2728 0.93 31.94243-100 583.02 435.509-11100 434.40992-31585

Subtyping

SCUEAL usage summary as of Mon Jun 18 00:00:56 2018 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days58145814.00 82.2140-500
Last 7 days5814830.57 82.2140-500
Last 30 days5814193.80 82.2140-500
Lifetime (3272 days)7118 2.18 87.6450-500

Top 10 Subtypes (out of 623813 sequences)

SubtypesTimes found% found
B242689 38.9
C107510 17.2
G44858 7.2
A139606 6.3
Complex25884 4.1
AE17995 2.9
D17108 2.7
CRF1411694 1.9
F19791 1.6
B,C recombinant8113 1.3

Coevolution

BGM usage summary as of Mon Jun 18 00:00:58 2018 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days3 3.00 61.676555-65 0.69 0.67 0.63- 0.75 166.67147106-247
Last 7 days9 1.29 43.67556-65 0.56 0.67 0.09- 0.75 98.331061-259
Last 30 days13 0.43 40.69386-65 0.83 0.67 0.09- 2.82 77.54511-259
Lifetime (1866 days)8720 4.67 64.76300-1033 2.26 0.98 0.01-263 2909.62 95.500-2900666

UCSD Viral Evolution Group 2004-2018