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SLAC

SLAC usage summary as of Tue Jul 14 00:00:01 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3523 days)92479 26.25 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 Jul 14 00:00:14 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days3 3.00322828-40 1273.3312731273-1274 3456.6730912331-4948
Last 7 days15 2.14 57.07285-334 1401.401273183-3304 4514.6035071017-11072
Last 30 days50 1.67 46.34223-334 782.80 433.5079-3433 2251.22 1387.50213-11072
Lifetime (2623 days)103365 39.41 44.51243-787 486.983251-11276 177.33460-51470

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8546917 45.4
REV13299 12.9
TRN9310127 9.8
F815368 5.2
0100003929 3.8
0102322092 2.0
0120121582 1.5
0122121394 1.3
0102301268 1.2
0120321002 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.083561 80.8
0.05 0.9 19.115309 14.8
0.2 2.1 29.72131 2.1
0.25 3.1 31.8932 0.9
0.01 0.4 14.7522 0.5
0.5 5.9 43.2214 0.2
0.15 2.3 21.7174 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 Jul 14 00:00:27 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days4 0.5713 11.506-23895 612.50538-1817 1752.25988185-4848
Last 30 days55 1.83 18.05116-74 512.6421976-1951 511.1117841-5604
Lifetime (2622 days)57825 22.05 20.70162-110 487.073231-10798 390.561110-54132

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8530763 53.2
REV5694 9.8
F813507 6.1
TRN933354 5.8
0100002341 4.0
0120121205 2.1
001101730 1.3
010232707 1.2
012212704 1.2
012032614 1.1
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.852259 90.4
100 4.4 22.11318 2.3
90 19.2 11.2901 1.6
20 7.2 35.8822 1.4
95 2.4 31.6764 1.3
10 5.8 31.9747 1.3
40 2.5 24.4145 0.3
25 7.8 34.6114 0.2
80 3.0 28.0109 0.2
30 10.0 20.291 0.2

TOGGLE

Toggle usage summary as of Tue Jul 14 00:00:34 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days1 0.03222222-22219219219-219394394394-394
Lifetime (3703 days)1088 0.29 47.56377-150 569.2535016-3789 3770.49 1970.5031-42841

Model Select.

ModelSelection usage summary as of Tue Jul 14 00:00:35 2020 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days14 2.00 18.57115-105 1306.86 1033.50183-4405
Last 30 days101 3.37 33.90135-305 660.3235476-9744
Lifetime (2623 days)101935 38.86 43.83223-656 521.633251-11935

Top 10 Models

ModelTimes selected% selected
HKY8524474 24.0
TRN9313078 12.8
F818844 8.7
0102324361 4.3
0120123561 3.5
0122123059 3.0
0102302481 2.4
0120322419 2.4
0122322417 2.4
0011012111 2.1

Protein Model Select.

ModelSelectionP usage summary as of Tue Jul 14 00:00:45 2020 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days3 0.10 148.671515-416 169.33192124-192
Lifetime (4424 days)3933 0.89 46.56252-500 670.434443-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F567 14.4
JTT (Jones,Taylor,Thornton)409 10.4
BLOSUM62+F326 8.3
WAG (Whelan and Goldman)+F323 8.2
HIV (within host)+F269 6.8
WAG (Whelan and Goldman)245 6.2
IAV (Influenza A virus)+F242 6.2
IAV (Influenza A virus)228 5.8
BLOSUM62169 4.3
LG (Le and Gascuel)166 4.2

GARD

GARD usage summary as of Tue Jul 14 00:00:47 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days6 0.86131210-17 2850.50 3100.501815-31952140 2176.50330-3833
Last 30 days39 1.30 18.67165-80 2225.462778192-3303 1634.28871182-3928
Lifetime (4976 days)75657 15.20 26.93182-300 2039.92111620-46625 1290.833851-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
063968 84.6
HKY855991 7.9
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
0-1027507 36.4
10-203009 4.0
20-302436 3.2
30-402266 3.0
40-501861 2.5
50-601969 2.6
60-701444 1.9
70-801322 1.7
80-901219 1.6
90-1001084 1.4
> 10031540 41.7
Number of breakpointsTimes found% found
023150 30.6
119131 25.3
212002 15.9
36972 9.2
44258 5.6
52922 3.9
61892 2.5
71416 1.9
8938 1.2
9761 1.0
≥ 102215 2.9

SBP

SBP usage summary as of Tue Jul 14 00:00:56 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00202202202-202111-1968968968-968
Last 7 days2 0.29 111.50 111.5021-202111-1946946924-968
Last 30 days18 0.60 76.56156-338 54.50711-161 341.8984-1049
Lifetime (2623 days)21089 8.04 50.12252-656 21.7511-45015 601.07430-683633

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8515287 72.5
REV1315 6.2
010000565 2.7
F81503 2.4
TRN93502 2.4
0123455266 1.3
010232215 1.0
012012137 0.6
0112304567120 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-109137 43.3
10-20909 4.3
20-30800 3.8
30-40654 3.1
40-50515 2.4
50-60412 2.0
60-70360 1.7
70-80377 1.8
80-90290 1.4
90-100321 1.5
> 1007314 34.7

PARRIS

PARRIS usage summary as of Tue Jul 14 00:00:59 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days30 1.00 12.731110-22 192.70175109-400 44.17 24.508-187
Lifetime (4731 days)14552 3.08 20.11153-75 488.813297-11903 425.901371-48648

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858226 56.5
F811077 7.4
REV1010 6.9
TRN93769 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
0-0.12663 18.3
0.1-0.2515 3.5
0.2-0.3472 3.2
0.3-0.4369 2.5
0.4-0.5331 2.3
0.5-0.6391 2.7
0.6-0.7373 2.6
0.7-0.8359 2.5
0.8-0.9355 2.4
0.9-18724 60.0

GA Branch

GABranch usage summary as of Tue Jul 14 00:01:01 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days1 0.03151515-15123123123-123492492492-492
Lifetime (4724 days)11823 2.50 13.73123-30 520.573339-11628 5643.3815101-889396

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858550 72.3
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
24308 36.4
34002 33.8
42219 18.8
5777 6.6
6236 2.0
7118 1.0
839 0.3
925 0.2

CMS

CMS usage summary as of Tue Jul 14 00:01:03 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14727272-72100510051005-1005108737108737108737-108737
Last 30 days8 0.27 33.38 37.5012-72 425.38 400.50123-100535687.1223765952-108737
Lifetime (3815 days)3266 0.86 33.70243-120 568.383437-1127621118.97403159-3262277

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10192 5.9
10-20151 4.6
20-30191 5.8
30-40222 6.8
40-50246 7.5
50-60179 5.5
60-70176 5.4
70-80129 3.9
80-90177 5.4
90-100111 3.4
> 1001492 45.7
Number of rate classesTimes found% found
10 0.0
22053 62.9
3716 21.9
4278 8.5
5117 3.6
650 1.5
715 0.5
82 0.1
91 0.0
≥ 1034 1.0

DEPS

DEPS usage summary as of Tue Jul 14 00:01:04 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days10 1.43 34.203527-38127412741274-1274 145.60 138.5092-209
Last 30 days114 3.80 45.204615-51 1009.861000192-1274 209.4019225-528
Lifetime (3694 days)3558 0.96 35.76 31.503-100 710.705269-11100 489.86 145.502-31585

Subtyping

SCUEAL usage summary as of Tue Jul 14 00:01:06 2020 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days66446644.00 84.1040-500
Last 7 days6644949.14 84.1040-500
Last 30 days6644221.47 84.1040-500
Lifetime (4029 days)7948 1.97 88.6550-500

Top 10 Subtypes (out of 704602 sequences)

SubtypesTimes found% found
B263343 37.4
C144342 20.5
G46814 6.6
A142427 6.0
Complex28830 4.1
AE19960 2.8
D19014 2.7
CRF1411765 1.7
F110663 1.5
B,C recombinant9472 1.3

Coevolution

BGM usage summary as of Tue Jul 14 00:01:08 2020 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (2623 days)8881 3.39 65.10300-1033 2.25 0.98 0.01-263 2866.47920-2900666

UCSD Viral Evolution Group 2004-2020