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SLAC

SLAC usage summary as of Fri Feb 22 00:00:02 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days20 20.0028325-53 391.6532386-756 5.86 5.36 0.67- 32.23
Last 7 days77 11.00 34.91315-248 482.6956686-756 4.64 2.50 0.48- 42.37
Last 30 days398 13.27 140.64803-434 588.8246682-3391 31.79 8.88 0.26- 141.61
Lifetime (3015 days)91720 30.42 52.78253-684 490.003251-11903 21.24 6.17 0.16- 7571.98

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8547105 51.4
TRN9313415 14.6
REV9497 10.4
F814209 4.6
0120121071 1.2
0102301070 1.2
0122121031 1.1
0102321003 1.1
012232848 0.9
012032755 0.8
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 0.6 16.276461 83.4
0.05 0.5 14.111418 12.4
0.2 0.9 18.41380 1.5
0.25 2.2 24.8775 0.8
0.5 4.4 56.0646 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 Fri Feb 22 00:00:14 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days13 13.00 24.77215-43 426.69323226-6641304919-435
Last 7 days64 9.14 30.12285-80 516.23566138-2061 107.384419-808
Last 30 days159 5.30 33.50193-287 703.7943182-3391 177.06465-2456
Lifetime (2115 days)100570 47.55 44.26243-787 481.823251-11276 142.97440-26278

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8545202 44.9
REV13083 13.0
TRN939929 9.9
F815159 5.1
0100003926 3.9
0102322058 2.0
0120121549 1.5
0122121365 1.4
0102301223 1.2
012032985 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.281280 80.8
0.05 0.9 19.114923 14.8
0.2 2.1 29.92063 2.1
0.25 3.2 32.7898 0.9
0.01 0.4 14.7520 0.5
0.5 5.9 42.8207 0.2
0.15 2.5 23.5161 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 Fri Feb 22 00:00:28 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days6 6.00 25.33 26.505-43 450.83 424.50303-664 620.83 121.5068-1901
Last 7 days20 2.86 27.35 21.504-44 476.60562124-664 242.15 84.5016-1901
Last 30 days80 2.67 17.82 17.503-44 500.7935856-2032 223.51 82.503-2233
Lifetime (2114 days)55965 26.47 20.62162-110 483.963211-10798 368.531090-50486

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8529565 52.8
REV5630 10.1
TRN933290 5.9
F813278 5.9
0100002336 4.2
0120121172 2.1
001101725 1.3
012212693 1.2
010232689 1.2
012032595 1.1
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.850567 90.4
100 4.2 22.51296 2.3
90 19.4 11.1890 1.6
20 7.2 36.0819 1.5
10 5.8 31.7741 1.3
95 2.2 30.7700 1.3
40 2.5 24.4145 0.3
80 3.0 28.0109 0.2
30 10.0 20.291 0.2
25 3.4 36.786 0.2

TOGGLE

Toggle usage summary as of Fri Feb 22 00:00:35 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3195 days)1072 0.34 47.53377-150 569.7935016-3789 3752.07 1961.5031-42841

Model Select.

ModelSelection usage summary as of Fri Feb 22 00:00:36 2019 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days16 16.00 23.69285-32 338.6932389-566
Last 7 days31 4.43 21.06215-35 393.5232346-2011
Last 30 days323 10.77 164.001133-434 538.5244846-11125
Lifetime (2115 days)98759 46.69 42.65223-656 517.713251-11935

Top 10 Models

ModelTimes selected% selected
HKY8523764 24.1
TRN9312830 13.0
F818570 8.7
0102324269 4.3
0120123419 3.5
0122122952 3.0
0102302356 2.4
0120322334 2.4
0122322321 2.4
0011012072 2.1

Protein Model Select.

ModelSelectionP usage summary as of Fri Feb 22 00:00:45 2019 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14191919-19370370370-370
Last 30 days6 0.20 39.17 19.5013-146 525.17546293-730
Lifetime (3916 days)3820 0.98 45.87252-499 650.504443-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F559 14.6
JTT (Jones,Taylor,Thornton)403 10.5
BLOSUM62+F323 8.5
WAG (Whelan and Goldman)+F318 8.3
WAG (Whelan and Goldman)244 6.4
IAV (Influenza A virus)+F238 6.2
HIV (within host)+F236 6.2
IAV (Influenza A virus)218 5.7
BLOSUM62167 4.4
LG (Le and Gascuel)161 4.2

GARD

GARD usage summary as of Fri Feb 22 00:00:47 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days4 4.0023285-31 734.25546267-1578 2125.752045330-4083
Last 7 days6 0.86 24.33285-3511411062267-2220 2322.67 2716.50330-4083
Last 30 days68 2.27 16.01113-49 2661.34 1240.50168-10302 1668.40 1073.5098-4083
Lifetime (4468 days)74520 16.68 26.84182-300 2029.15 1110.5020-46625 1271.053751-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
062831 84.3
HKY855991 8.0
010000860 1.2
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
0-1027083 36.3
10-202985 4.0
20-302409 3.2
30-402237 3.0
40-501843 2.5
50-601946 2.6
60-701421 1.9
70-801311 1.8
80-901203 1.6
90-1001076 1.4
> 10031006 41.6
Number of breakpointsTimes found% found
022765 30.5
118904 25.4
211802 15.8
36820 9.2
44164 5.6
52883 3.9
61865 2.5
71407 1.9
8934 1.3
9761 1.0
≥ 102215 3.0

SBP

SBP usage summary as of Fri Feb 22 00:00:56 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days3 0.43 121.675435-276 4.3321-10 6190.67970113-17489
Last 30 days13 0.43 42.31167-276 10.8521-96 1598.771134-17489
Lifetime (2115 days)20461 9.67 49.01242-656 21.6811-45015 480.02410-279793

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8514744 72.1
REV1315 6.4
010000565 2.8
F81503 2.5
TRN93502 2.5
0123455228 1.1
010232215 1.1
012012137 0.7
0112304567115 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-108836 43.2
10-20895 4.4
20-30787 3.8
30-40636 3.1
40-50506 2.5
50-60405 2.0
60-70352 1.7
70-80374 1.8
80-90281 1.4
90-100310 1.5
> 1007079 34.6

PARRIS

PARRIS usage summary as of Fri Feb 22 00:00:59 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00777-7868686-86858585-85
Last 7 days2 0.29 30.50 30.507-54 381.50 381.5086-6771198119885-2311
Last 30 days7 0.23 20.57117-54 950.5767786-203266336064-2311
Lifetime (4223 days)14258 3.38 20.18153-75 485.623297-11903 414.021371-35284

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858049 56.5
F811063 7.5
REV1001 7.0
TRN93747 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
0-0.12608 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
0.9-18544 59.9

GA Branch

GABranch usage summary as of Fri Feb 22 00:01:01 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00161616-16520520520-520101331013310133-10133
Last 7 days1 0.14161616-16520520520-520101331013310133-10133
Last 30 days4 0.13 12.751211-1612291276332-203210470117372927-15479
Lifetime (4216 days)11683 2.77 13.72123-30 516.673309-11628 5304.1115131-636439

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858412 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
24269 36.5
33949 33.8
42194 18.8
5769 6.6
6232 2.0
7113 1.0
835 0.3
923 0.2

CMS

CMS usage summary as of Fri Feb 22 00:01:02 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days2 2.00323232-32323323323-32310124101248763-11485
Last 7 days2 0.29323232-32323323323-32310124101248763-11485
Last 30 days8 0.27 23.622611-39 2337.75 1098.50323-1112522734.2510835.504733-71649
Lifetime (3307 days)3144 0.95 33.69243-120 542.313387-1127617725.91394259-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10184 5.9
10-20146 4.6
20-30188 6.0
30-40214 6.8
40-50240 7.6
50-60177 5.6
60-70170 5.4
70-80127 4.0
80-90175 5.6
90-100108 3.4
> 1001415 45.0
Number of rate classesTimes found% found
10 0.0
21993 63.4
3693 22.0
4256 8.1
5106 3.4
646 1.5
714 0.4
82 0.1
90 0.0
≥ 1034 1.1

DEPS

DEPS usage summary as of Fri Feb 22 00:01:03 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days9 0.30 33.562013-90 617.78535288-1199 450.1120684-1507
Lifetime (3186 days)3107 0.98 34.08273-100 618.344829-11100 502.841252-31585

Subtyping

SCUEAL usage summary as of Fri Feb 22 00:01:03 2019 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days60066006.00 82.9140-500
Last 7 days6006858.00 82.9140-500
Last 30 days6006200.20 82.9140-500
Lifetime (3521 days)7310 2.08 88.0750-500

Top 10 Subtypes (out of 643769 sequences)

SubtypesTimes found% found
B252038 39.2
C109188 17.0
G45646 7.1
A140635 6.3
Complex26819 4.2
AE18955 2.9
D18642 2.9
CRF1411733 1.8
F110111 1.6
B,C recombinant8360 1.3

Coevolution

BGM usage summary as of Fri Feb 22 00:01:05 2019 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00111111-11111-1444-4
Last 7 days1 0.14111111-11111-1444-4
Last 30 days33 1.10 99.301123-415 1.28 0.27 0.16- 16.90 532.67631-8123
Lifetime (2115 days)8879 4.20 65.11300-1033 2.25 0.98 0.01-263 2867.12930-2900666

UCSD Viral Evolution Group 2004-2019