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SLAC

SLAC usage summary as of Mon Dec 17 00:00:02 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00888-8387387387-387 1.02 1.02 1.02- 1.02
Last 7 days136 19.43 17.20 7.503-296 569.8233453-3957 2.98 1.08 0.32- 42.52
Last 30 days669 22.30 31.49203-485 482.123637-3957 9.29 4.56 0.32- 234.63
Lifetime (2948 days)90850 30.82 52.14253-684 488.853251-11903 21.18 6.16 0.16- 7571.98

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8546789 51.5
TRN9313348 14.7
REV9460 10.4
F814141 4.6
0102301048 1.2
0120121040 1.1
0102321000 1.1
012212996 1.1
012232798 0.9
012032740 0.8
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 0.6 16.276010 83.7
0.05 0.5 14.411067 12.2
0.2 0.9 18.01364 1.5
0.25 2.2 24.9763 0.8
0.5 4.4 56.0646 0.7
0.01 0.8 9.6532 0.6
0.15 2.4 14.4107 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 Mon Dec 17 00:00:14 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days3 3.00 138.672048-20418732616387-2616 3625.33534615-5515
Last 7 days68 9.71 24.01 7.504-207 673.3834353-3957 388.81245-7951
Last 30 days239 7.97 35.07124-485 610.4344353-3957 363.15375-11479
Lifetime (2048 days)99928 48.79 44.21243-787 480.523251-11276 141.36440-26278

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8544895 44.9
REV13020 13.0
TRN939875 9.9
F815081 5.1
0100003923 3.9
0102322052 2.1
0120121523 1.5
0122121363 1.4
0102301223 1.2
012032971 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.280768 80.8
0.05 0.9 19.214886 14.9
0.2 2.1 29.52039 2.0
0.25 3.2 32.8883 0.9
0.01 0.4 14.6514 0.5
0.5 5.9 42.8207 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 Mon Dec 17 00:00:27 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days32 4.57 10.0374-28 619.25 382.5053-2332 232.84 67.504-1975
Last 30 days119 3.97 15.70104-49 688.4344353-4980 288.501364-6683
Lifetime (2047 days)55620 27.17 20.60162-110 483.063211-10798 365.661080-39109

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8529374 52.8
REV5628 10.1
TRN933274 5.9
F813244 5.8
0100002336 4.2
0120121147 2.1
001101725 1.3
012212690 1.2
010232689 1.2
012032581 1.0
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.750235 90.3
100 4.2 22.51294 2.3
90 19.4 11.1890 1.6
20 7.2 36.0818 1.5
10 5.7 31.8735 1.3
95 2.2 30.8698 1.3
40 2.5 24.4145 0.3
80 3.1 28.2108 0.2
30 10.0 20.291 0.2
25 3.4 36.786 0.2

TOGGLE

Toggle usage summary as of Mon Dec 17 00:00:33 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29 19.50 19.5011-28 2171.50 2171.502011-2332235223522183-2521
Last 30 days3 0.10 19.331911-28222523322011-2332 2253.6721832057-2521
Lifetime (3128 days)1072 0.34 47.53377-150 569.7935016-3789 3752.07 1961.5031-42841

Model Select.

ModelSelection usage summary as of Mon Dec 17 00:00:34 2018 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days2 2.00 54.50 54.507-102 449.50 449.50133-766
Last 7 days48 6.86 25.08 12.503-296522 305.5068-2333
Last 30 days694 23.13 28.28153-485 468.07 332.507-3945
Lifetime (2048 days)97875 47.79 41.92223-656 516.723251-11935

Top 10 Models

ModelTimes selected% selected
HKY8523591 24.1
TRN9312792 13.1
F818505 8.7
0102324244 4.3
0120123377 3.5
0122122911 3.0
0102302315 2.4
0120322304 2.4
0122322205 2.3
0011012069 2.1

Protein Model Select.

ModelSelectionP usage summary as of Mon Dec 17 00:00:42 2018 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days9 0.30 35.563310-59433224224-1238
Lifetime (3849 days)3802 0.99 45.91252-499 651.724443-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F554 14.6
JTT (Jones,Taylor,Thornton)403 10.6
BLOSUM62+F321 8.4
WAG (Whelan and Goldman)+F316 8.3
WAG (Whelan and Goldman)243 6.4
IAV (Influenza A virus)+F238 6.3
HIV (within host)+F235 6.2
IAV (Influenza A virus)218 5.7
BLOSUM62166 4.4
LG (Le and Gascuel)161 4.2

GARD

GARD usage summary as of Mon Dec 17 00:00:44 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days17 2.43 21.5983-146 3299.291734435-11871 1387.59988101-3753
Last 30 days242 8.07 20.27103-261 1618.521077252-11871 1258.94 580.5089-13569
Lifetime (4401 days)74393 16.90 26.84182-300 2027.89111020-46625 1270.233741-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
062704 84.3
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
0-1027032 36.3
10-202985 4.0
20-302409 3.2
30-402235 3.0
40-501838 2.5
50-601945 2.6
60-701413 1.9
70-801305 1.8
80-901200 1.6
90-1001074 1.4
> 10030957 41.6
Number of breakpointsTimes found% found
022721 30.5
118882 25.4
211782 15.8
36809 9.2
44154 5.6
52867 3.9
61861 2.5
71407 1.9
8934 1.3
9761 1.0
≥ 102215 3.0

SBP

SBP usage summary as of Mon Dec 17 00:00:53 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days13 1.86 37.77413-67 1.5411-6 197.8516912-622
Last 30 days72 2.40 46.67153-485 3.2111-38 405.61 34.502-4869
Lifetime (2048 days)20436 9.98 48.95242-656 21.6411-45015 478.62410-279793

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8514720 72.0
REV1315 6.4
010000565 2.8
F81503 2.5
TRN93502 2.5
0123455227 1.1
010232215 1.1
012012137 0.7
0112304567115 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-108823 43.2
10-20895 4.4
20-30787 3.9
30-40636 3.1
40-50506 2.5
50-60403 2.0
60-70352 1.7
70-80374 1.8
80-90281 1.4
90-100308 1.5
> 1007071 34.6

PARRIS

PARRIS usage summary as of Mon Dec 17 00:00:56 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days4 0.57 10.25118-11 1610.252011387-2032 817.25 911.508-1438
Last 30 days16 0.5319184-39 945.8179490-2332 466.56 344.508-1438
Lifetime (4156 days)14250 3.43 20.18153-75 485.253297-11903 413.861371-35284

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858045 56.5
F811063 7.5
REV1000 7.0
TRN93746 5.2
010000429 3.0
012012252 1.8
001101166 1.2
012212154 1.1
012032128 0.9
010230120 0.8
p-values rangeTimes found% found
0-0.12607 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 2.4
0.9-18537 59.9

GA Branch

GABranch usage summary as of Mon Dec 17 00:00:58 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29998-10447447387-507602602356-848
Last 30 days4 0.13 11.25108-17 664.25447219-1544 5662.75 2315.50356-17664
Lifetime (4149 days)11674 2.81 13.72123-30 515.763309-11628 5299.11 1510.501-636439

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858403 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
24268 36.6
33947 33.8
42192 18.8
5766 6.6
6231 2.0
7113 1.0
835 0.3
923 0.2

CMS

CMS usage summary as of Mon Dec 17 00:00:59 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days4 0.57 14.50118-28 1690.50 2021.50387-233220368.254118490-72747
Last 30 days8 0.27 28.12188-92 1248.38 1297.5090-233213757.255709490-72747
Lifetime (3240 days)3132 0.97 33.68243-120 537.993387-1127617713.59 3915.5059-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10184 5.9
10-20145 4.6
20-30188 6.0
30-40214 6.8
40-50240 7.7
50-60176 5.6
60-70170 5.4
70-80127 4.1
80-90174 5.6
90-100107 3.4
> 1001407 44.9
Number of rate classesTimes found% found
10 0.0
21986 63.4
3689 22.0
4256 8.2
5105 3.4
646 1.5
714 0.4
82 0.1
90 0.0
≥ 1034 1.1

DEPS

DEPS usage summary as of Mon Dec 17 00:00:59 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14777777-77759759759-759148148148-148
Last 30 days25 0.83 63.765917-98 445.24252224-1238 260.6421158-960
Lifetime (3119 days)3091 0.99 34.04273-100 619.274839-11100 503.611252-31585

Subtyping

SCUEAL usage summary as of Mon Dec 17 00:01:00 2018 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days59605960.00 82.9940-500
Last 7 days5960851.43 82.9940-500
Last 30 days5960198.67 82.9940-500
Lifetime (3454 days)7264 2.10 88.1750-500

Top 10 Subtypes (out of 640438 sequences)

SubtypesTimes found% found
B250792 39.2
C109030 17.0
G45597 7.1
A140578 6.3
Complex26447 4.1
D18621 2.9
AE18482 2.9
CRF1411731 1.8
F110087 1.6
B,C recombinant8158 1.3

Coevolution

BGM usage summary as of Mon Dec 17 00:01:02 2018 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days6 0.869422-525 4.84 3.37 0.79-10 433.50180-2458
Last 30 days17 0.57 125.24172-525 2.75 1.52 0.22-10 896.59820-5966
Lifetime (2048 days)8838 4.32 64.82300-1033 2.25 0.98 0.01-263 2877.69930-2900666

UCSD Viral Evolution Group 2004-2018