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SLAC

SLAC usage summary as of Wed Oct 17 00:00:01 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days15 15.00 29.20213-115 327.6723581-820 5.21 1.96 0.37- 18.89
Last 7 days161 23.00 38.10153-486 428.5121952-3721 8.32 2.25 0.29- 84.29
Last 30 days547 18.23 55.52183-499 407.962986-4390 12.12 2.43 0.23- 209.14
Lifetime (2887 days)89762 31.09 52.09253-684 488.483251-11903 21.26 6.18 0.16- 7571.98

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8546375 51.7
TRN9313237 14.7
REV9420 10.5
F814047 4.5
0102301039 1.2
010232992 1.1
012212967 1.1
012012926 1.0
012232779 0.9
010210693 0.8
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 0.6 16.275146 83.7
0.05 0.5 14.510912 12.2
0.2 0.9 18.11359 1.5
0.25 2.2 25.3751 0.8
0.5 4.4 55.7617 0.7
0.01 0.8 9.4527 0.6
0.15 2.5 15.0103 0.1
0.3 0.2 19.247 0.1
0.0024 0.0 2.345 0.1
0.0048 0.0 0.533 0.0

FEL

FEL usage summary as of Wed Oct 17 00:00:12 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days6 6.00 68.676925-115 603.67610235-820 278.50256185-442
Last 7 days84 12.00 37.611710-499 503.1541752-3721 260.86637-4353
Last 30 days315 10.50 31.26173-499 398.3930110-3721 133.57504-4353
Lifetime (1987 days)99357 50.00 44.24243-787 479.233251-11276 140.61440-26278

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8544648 44.9
REV13005 13.1
TRN939825 9.9
F814991 5.0
0100003923 3.9
0102322047 2.1
0120121471 1.5
0122121342 1.4
0102301217 1.2
012032964 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.280328 80.8
0.05 0.9 19.214792 14.9
0.2 2.1 29.62036 2.0
0.25 3.2 33.0876 0.9
0.01 0.5 14.3504 0.5
0.5 5.4 43.6198 0.2
0.15 2.6 22.7154 0.2
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 Oct 17 00:00:25 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days5 5.00 29.803123-35 800.40820672-891 226.40197173-373
Last 7 days60 8.57 21.80 16.5010-75 523.80 414.5052-5285 260.4511710-2626
Last 30 days181 6.03 23.52173-75 394.3627110-5285 208.12921-2626
Lifetime (1986 days)55299 27.84 20.63162-110 481.703191-10798 366.211080-39109

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8529248 52.9
REV5620 10.2
TRN933258 5.9
F813187 5.8
0100002336 4.2
0120121095 2.0
001101725 1.3
010232687 1.2
012212674 1.2
012032577 1.0
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.849945 90.3
100 4.2 22.61285 2.3
90 19.4 11.1890 1.6
20 7.3 36.2808 1.5
10 5.7 31.8735 1.3
95 2.2 30.8694 1.3
40 2.5 24.4145 0.3
80 3.0 28.5107 0.2
30 10.0 20.291 0.2
25 2.3 37.185 0.2

TOGGLE

Toggle usage summary as of Wed Oct 17 00:00:31 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days1 0.03585858-58174174174-174310310310-310
Lifetime (3067 days)1068 0.35 47.53377-150 565.4035016-3789 3756.52 1919.5031-42841

Model Select.

ModelSelection usage summary as of Wed Oct 17 00:00:32 2018 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days20 20.00 29.55213-115 349.17 186.5075-820
Last 7 days140 20.00 33.37183-207 478.02 289.5052-5285
Last 30 days473 15.77 52.58183-484 415.2729810-5285
Lifetime (1987 days)96715 48.67 41.90223-656 515.753251-11935

Top 10 Models

ModelTimes selected% selected
HKY8523296 24.1
TRN9312706 13.1
F818428 8.7
0102324234 4.4
0120123231 3.3
0122122874 3.0
0102302301 2.4
0120322214 2.3
0122322182 2.3
0011012053 2.1

Protein Model Select.

ModelSelectionP usage summary as of Wed Oct 17 00:00:41 2018 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14151515-15136136136-136
Last 30 days3 0.10 21.671515-35 239.67223136-360
Lifetime (3788 days)3779 1.00 45.96252-499 652.404443-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F550 14.6
JTT (Jones,Taylor,Thornton)400 10.6
BLOSUM62+F318 8.4
WAG (Whelan and Goldman)+F311 8.2
WAG (Whelan and Goldman)241 6.4
IAV (Influenza A virus)+F235 6.2
HIV (within host)+F235 6.2
IAV (Influenza A virus)217 5.7
BLOSUM62165 4.4
LG (Le and Gascuel)161 4.3

GARD

GARD usage summary as of Wed Oct 17 00:00:42 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days6 0.86 41.173218-7511611059408-2358 1532.67888316-4225
Last 30 days25 0.83 54.72377-156 2196.521269231-8359 2376.2490068-9511
Lifetime (4340 days)74081 17.07 26.87182-300 2028.85111020-46625 1270.543741-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
062392 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
0-1026907 36.3
10-202950 4.0
20-302390 3.2
30-402219 3.0
40-501826 2.5
50-601943 2.6
60-701405 1.9
70-801301 1.8
80-901195 1.6
90-1001071 1.4
> 10030874 41.7
Number of breakpointsTimes found% found
022618 30.5
118785 25.4
211740 15.8
36782 9.2
44132 5.6
52852 3.8
61855 2.5
71407 1.9
8934 1.3
9761 1.0
≥ 102215 3.0

SBP

SBP usage summary as of Wed Oct 17 00:00:51 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29 30.50 30.5022-39 5.50 5.503-8 21.50 21.502-41
Last 30 days14 0.47 45.794012-151 18.5711-203 289.93800-1041
Lifetime (1987 days)20341 10.24 48.86242-656 21.7211-45015 477.24410-279793

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8514629 71.9
REV1315 6.5
010000565 2.8
TRN93501 2.5
F81501 2.5
0123455227 1.1
010232215 1.1
012012137 0.7
0112304567115 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-108788 43.2
10-20892 4.4
20-30780 3.8
30-40629 3.1
40-50504 2.5
50-60403 2.0
60-70351 1.7
70-80374 1.8
80-90281 1.4
90-100300 1.5
> 1007039 34.6

PARRIS

PARRIS usage summary as of Wed Oct 17 00:00:55 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days2 2.00252523-27 805.50 805.50720-891 500.50 500.50240-761
Last 7 days6 0.86222118-27 774.33868154-1018 396.50 236.50196-761
Last 30 days15 0.50 20.93189-58 675.40845154-1049 236.1319661-761
Lifetime (4095 days)14229 3.47 20.18153-75 484.643297-11903 413.921361-35284

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858034 56.5
F811061 7.5
REV1000 7.0
TRN93745 5.2
010000429 3.0
012012251 1.8
001101166 1.2
012212153 1.1
012032127 0.9
010230120 0.8
p-values rangeTimes found% found
0-0.12606 18.3
0.1-0.2504 3.5
0.2-0.3460 3.2
0.3-0.4361 2.5
0.4-0.5326 2.3
0.5-0.6389 2.7
0.6-0.7364 2.6
0.7-0.8353 2.5
0.8-0.9349 2.5
0.9-18517 59.9

GA Branch

GABranch usage summary as of Wed Oct 17 00:00:56 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29141412-16 503.50 503.50122-885 7564.50 7564.504760-10369
Last 30 days2 0.07141412-16 503.50 503.50122-885 7564.50 7564.504760-10369
Lifetime (4088 days)11663 2.85 13.72123-30 515.933309-11628 5301.9115131-636439

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858392 72.0
REV614 5.3
010000568 4.9
F81415 3.6
TRN93283 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
24259 36.5
33946 33.8
42191 18.8
5766 6.6
6231 2.0
7113 1.0
835 0.3
923 0.2

CMS

CMS usage summary as of Wed Oct 17 00:00:58 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days3 0.10 48.334938-58 130.3314077-174987273353707-18574
Lifetime (3179 days)3119 0.98 33.67243-120 536.343387-1127617733.73390559-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10183 5.9
10-20143 4.6
20-30188 6.0
30-40213 6.8
40-50239 7.7
50-60175 5.6
60-70170 5.5
70-80127 4.1
80-90172 5.5
90-100107 3.4
> 1001402 45.0
Number of rate classesTimes found% found
10 0.0
21977 63.4
3686 22.0
4256 8.2
5104 3.3
646 1.5
714 0.4
82 0.1
90 0.0
≥ 1034 1.1

DEPS

DEPS usage summary as of Wed Oct 17 00:00:59 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days13 0.43 59.545933-97 389.77230223-757 4217.54126373-19670
Lifetime (3058 days)3050 1.00 33.70273-100 620.824839-11100 480.68 123.502-31585

Subtyping

SCUEAL usage summary as of Wed Oct 17 00:01:00 2018 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days59195919.00 83.3040-500
Last 7 days5919845.57 83.3040-500
Last 30 days5919197.30 83.3040-500
Lifetime (3393 days)7223 2.13 88.4650-500

Top 10 Subtypes (out of 638914 sequences)

SubtypesTimes found% found
B250377 39.2
C108903 17.0
G45560 7.1
A140506 6.3
Complex26146 4.1
D18612 2.9
AE18467 2.9
CRF1411731 1.8
F110058 1.6
B,C recombinant8145 1.3

Coevolution

BGM usage summary as of Wed Oct 17 00:01:02 2018 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14999-9 0.33 0.33 0.33- 0.33000-0
Last 30 days13 0.43 25.38103-154 2.351 0.15- 11.40 870.7700-8766
Lifetime (1987 days)8813 4.44 64.74300-1033 2.25 0.98 0.01-263 2884.00930-2900666

UCSD Viral Evolution Group 2004-2018