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SLAC

SLAC usage summary as of Thu Aug 16 00:00:02 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days5 5.00 34.202820-65 474.80510421-510 11.75 14.85 2.55- 19.20
Last 7 days91 13.00 40.69143-487 597.49548109-1369 13.06 5.49 0.34-205
Last 30 days292 9.73 51.40213-487 586.344476-3434 10.71 4.24 0.34-205
Lifetime (2825 days)88802 31.43 51.84253-684 488.933251-11903 21.31 6.20 0.16- 7571.98

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8545953 51.7
TRN9313190 14.9
REV9376 10.6
F813972 4.5
0102301002 1.1
010232985 1.1
012212940 1.1
012012879 1.0
012232762 0.9
012032662 0.7
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 0.6 16.274412 83.8
0.05 0.5 14.510738 12.1
0.2 0.9 17.71324 1.5
0.25 2.2 25.6739 0.8
0.5 4.4 55.7617 0.7
0.01 0.8 9.4526 0.6
0.15 2.5 15.2101 0.1
0.3 0.2 19.646 0.1
0.0024 0.0 2.345 0.1
0.0048 0.0 0.533 0.0

FEL

FEL usage summary as of Thu Aug 16 00:00:12 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days17 17.00 36.71346-65 484.29510252-575 84.068213-329
Last 7 days92 13.14 49.43154-48740735082-1487 145.66396-1925
Last 30 days337 11.23 50.70213-487 484.3435053-3434 122.84366-1995
Lifetime (1925 days)98800 51.32 44.29243-787 479.403251-11276 140.62440-26278

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8544444 45.0
REV12980 13.1
TRN939787 9.9
F814922 5.0
0100003921 4.0
0102322041 2.1
0120121437 1.5
0122121330 1.3
0102301203 1.2
001101948 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.279862 80.8
0.05 0.9 19.214732 14.9
0.2 2.1 29.42008 2.0
0.25 3.2 33.1873 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 Thu Aug 16 00:00:25 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days5 5.00 21.402012-39 721.20575421-1487 1074.40207155-4482
Last 7 days42 6.00 20.45 13.504-67 414.17350131-1487 262.9314011-4482
Last 30 days163 5.43 24.26203-75 550.043506-3434 612.9015010-4949
Lifetime (1924 days)55015 28.59 20.62162-110 482.103201-10798 364.501080-39109

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8529112 52.9
REV5608 10.2
TRN933244 5.9
F813155 5.7
0100002329 4.2
0120121080 2.0
001101723 1.3
010232684 1.2
012212668 1.2
012032567 1.0
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.749669 90.3
100 4.2 22.61284 2.3
90 19.4 11.1890 1.6
20 7.3 36.2808 1.5
10 5.7 32.0730 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 36.984 0.2

TOGGLE

Toggle usage summary as of Thu Aug 16 00:00:30 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days1 0.03212121-21566566566-566251251251-251
Lifetime (3005 days)1065 0.35 47.56377-150 566.0135016-3789 3763.81193231-42841

Model Select.

ModelSelection usage summary as of Thu Aug 16 00:00:32 2018 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days6 6.00 28.83166-65 387.67459119-542
Last 7 days71 10.14 28.97143-487 681.25667119-1487
Last 30 days320 10.67 53.70213-487 603.404876-3423
Lifetime (1925 days)95891 49.81 41.57223-656 516.273251-11935

Top 10 Models

ModelTimes selected% selected
HKY8523080 24.1
TRN9312650 13.2
F818409 8.8
0102324218 4.4
0120123157 3.3
0122122842 3.0
0102302257 2.4
0120322197 2.3
0122322155 2.2
0011012032 2.1

Protein Model Select.

ModelSelectionP usage summary as of Thu Aug 16 00:00:40 2018 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14777-7279279279-279
Last 30 days3 0.10 40.67367-79 268.67279102-425
Lifetime (3726 days)3772 1.01 45.98252-499 652.364443-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F549 14.6
JTT (Jones,Taylor,Thornton)399 10.6
BLOSUM62+F318 8.4
WAG (Whelan and Goldman)+F308 8.2
WAG (Whelan and Goldman)241 6.4
HIV (within host)+F235 6.2
IAV (Influenza A virus)+F235 6.2
IAV (Influenza A virus)217 5.8
BLOSUM62165 4.4
LG (Le and Gascuel)161 4.3

GARD

GARD usage summary as of Thu Aug 16 00:00:41 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days3 3.0019176-341040879756-1485 211.6726583-287
Last 7 days13 1.86 28.31306-53 1573.151584690-4461 811.0830983-3620
Last 30 days111 3.70 31.17225-170 1610.891056195-10302 679.6027983-3627
Lifetime (4278 days)74007 17.30 26.84182-300 2028.89111020-46625 1269.623741-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
062318 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
0-1026884 36.3
10-202948 4.0
20-302388 3.2
30-402216 3.0
40-501826 2.5
50-601943 2.6
60-701405 1.9
70-801300 1.8
80-901194 1.6
90-1001069 1.4
> 10030834 41.7
Number of breakpointsTimes found% found
022596 30.5
118756 25.3
211734 15.9
36781 9.2
44128 5.6
52848 3.8
61853 2.5
71403 1.9
8932 1.3
9761 1.0
≥ 102215 3.0

SBP

SBP usage summary as of Thu Aug 16 00:00:50 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14555-5111-1212121-21
Last 30 days13 0.43 92.54195-412 15.6951-127 658.69952-2838
Lifetime (1925 days)20298 10.54 48.88242-656 21.6611-45015 477.84410-279793

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8514593 71.9
REV1311 6.5
010000565 2.8
TRN93501 2.5
F81500 2.5
0123455225 1.1
010232215 1.1
012012137 0.7
0112304567115 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-108759 43.2
10-20891 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
> 1007026 34.6

PARRIS

PARRIS usage summary as of Thu Aug 16 00:00:52 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00202020-20421421421-421888888-88
Last 7 days11 1.57 21.642014-39 500.45546252-577 370.6427688-1466
Last 30 days22 0.73 20.18163-66 543.41 501.5069-1698 255.27 180.502-1466
Lifetime (4033 days)14208 3.52 20.18153-75 484.413297-11903 414.081361-35284

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858018 56.4
F811059 7.5
REV1000 7.0
TRN93743 5.2
010000429 3.0
012012250 1.8
001101166 1.2
012212153 1.1
012032127 0.9
010230120 0.8
p-values rangeTimes found% found
0-0.12603 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
0.5-0.6386 2.7
0.6-0.7364 2.6
0.7-0.8351 2.5
0.8-0.9346 2.4
0.9-18507 59.9

GA Branch

GABranch usage summary as of Thu Aug 16 00:00:54 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days4 0.5713146-18267252217-347 2004.75 2296.50138-3288
Last 30 days10 0.33 12.70144-18 441.10252217-1698 1604.30 1778.5020-3288
Lifetime (4026 days)11654 2.89 13.72123-30 515.913309-11628 5302.35 1511.501-636439

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858383 71.9
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
24258 36.5
33941 33.8
42191 18.8
5763 6.5
6231 2.0
7113 1.0
835 0.3
923 0.2

CMS

CMS usage summary as of Thu Aug 16 00:00:55 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days2 0.07161616-16169816981698-1698148314831380-1586
Lifetime (3117 days)3111 1.00 33.69243-120 536.463387-1127617737.49389659-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10183 5.9
10-20142 4.6
20-30188 6.0
30-40213 6.8
40-50239 7.7
50-60174 5.6
60-70170 5.5
70-80126 4.1
80-90172 5.5
90-100107 3.4
> 1001397 44.9
Number of rate classesTimes found% found
10 0.0
21974 63.5
3684 22.0
4256 8.2
5102 3.3
645 1.4
714 0.5
82 0.1
90 0.0
≥ 1034 1.1

DEPS

DEPS usage summary as of Thu Aug 16 00:00:56 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days1 0.03363636-36425425425-425321321321-321
Lifetime (2996 days)2754 0.92 32.30243-100 582.804449-11100 482.901012-31585

Subtyping

SCUEAL usage summary as of Thu Aug 16 00:00:57 2018 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days58515851.00 81.9940-500
Last 7 days5851835.86 81.9940-500
Last 30 days5851195.03 81.9940-500
Lifetime (3331 days)7155 2.15 87.4350-500

Top 10 Subtypes (out of 625556 sequences)

SubtypesTimes found% found
B243306 38.9
C107545 17.2
G44898 7.2
A140311 6.4
Complex25949 4.1
AE18002 2.9
D17127 2.7
CRF1411705 1.9
F19798 1.6
B,C recombinant8115 1.3

Coevolution

BGM usage summary as of Thu Aug 16 00:00:59 2018 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14333-3111-1111-1
Last 30 days15 0.50 143.332053-301 1.50 0.26 0.26- 7.42 1577.873851-17836
Lifetime (1925 days)8767 4.55 64.75300-1033 2.26 0.98 0.01-263 2896.98950-2900666

UCSD Viral Evolution Group 2004-2018