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SLAC

SLAC usage summary as of Wed Sep 30 00:00:01 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3601 days)92479 25.68 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 Wed Sep 30 00:00:23 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00191919-19286286286-286865865865-865
Last 7 days9 1.2929253-110 672.22556236-127428512748865-5999
Last 30 days93 3.10 21.28113-252 424.9227538-2201 1667.771205120-8204
Lifetime (2701 days)103568 38.34 44.51243-787 486.993251-11276 180.41460-51470

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8547063 45.4
REV13313 12.9
TRN9310130 9.8
F815391 5.2
0100003929 3.8
0102322092 2.0
0120121582 1.5
0122121394 1.3
0102301269 1.2
0120321004 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.083732 80.8
0.05 0.9 19.115327 14.8
0.2 2.1 29.72136 2.1
0.25 3.1 31.8937 0.9
0.01 0.4 14.7523 0.5
0.5 5.9 43.2214 0.2
0.15 2.3 21.9177 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 Wed Sep 30 00:00:37 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days5 5.0016194-1924028656-286 172.60165163-186
Last 7 days8 1.14 16.12194-31 380.6228656-1273 155.1216557-264
Last 30 days32 1.07 17.91 12.504-56 735.1928656-11542 276.6216543-2074
Lifetime (2700 days)57918 21.45 20.70162-110 487.213221-11542 390.451110-54132

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8530824 53.2
REV5697 9.8
F813514 6.1
TRN933354 5.8
0100002344 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 27.852350 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 34.7115 0.2
80 3.0 28.0109 0.2
30 10.0 20.291 0.2

TOGGLE

Toggle usage summary as of Wed Sep 30 00:00:44 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3781 days)1089 0.29 47.57377-150 569.0935016-3789 3770.96197331-42841

Model Select.

ModelSelection usage summary as of Wed Sep 30 00:00:45 2020 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days2 2.00 11.50 11.504-1917117156-286
Last 7 days60 8.57 18.93153-110 545.37 299.3356- 3878.67
Last 30 days102 3.40 20.49153-242 699.34 351.3356-11542
Lifetime (2701 days)102146 37.82 43.82223-656 522.203251-11935

Top 10 Models

ModelTimes selected% selected
HKY8524525 24.0
TRN9313093 12.8
F818870 8.7
0102324379 4.3
0120123566 3.5
0122123069 3.0
0102302483 2.4
0120322421 2.4
0122322420 2.4
0011012111 2.1

Protein Model Select.

ModelSelectionP usage summary as of Wed Sep 30 00:00:55 2020 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days1 0.03303030-30269269269-269
Lifetime (4502 days)3937 0.87 46.54252-500 672.574443-18120

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)+F324 8.2
HIV (within host)+F271 6.9
WAG (Whelan and Goldman)245 6.2
IAV (Influenza A virus)+F242 6.1
IAV (Influenza A virus)228 5.8
BLOSUM62169 4.3
LG (Le and Gascuel)166 4.2

GARD

GARD usage summary as of Wed Sep 30 00:00:56 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days5 5.00 20.40248-2431864791171-479128803681280-3701
Last 7 days19 2.71 22.95234-61 3546.631698168-11636 2281.473046280-3800
Last 30 days32 1.07 18.12223-61 5238.25 3781.50168-34626 2420.59 3621.50280-4591
Lifetime (5054 days)75740 14.99 26.94182-300 2042.90111620-46625 1291.853861-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
064051 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
0-1027523 36.3
10-203009 4.0
20-302438 3.2
30-402267 3.0
40-501868 2.5
50-601973 2.6
60-701449 1.9
70-801323 1.7
80-901220 1.6
90-1001085 1.4
> 10031585 41.7
Number of breakpointsTimes found% found
023165 30.6
119155 25.3
212016 15.9
36990 9.2
44258 5.6
52926 3.9
61897 2.5
71417 1.9
8940 1.2
9761 1.0
≥ 102215 2.9

SBP

SBP usage summary as of Wed Sep 30 00:01:06 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days25 3.57281514-165 1.9611-9 300.5634264-610
Last 30 days35 1.17 24.66153-165 7.2311-144 340.033088-1424
Lifetime (2701 days)21149 7.83 50.11252-656 21.7111-45015 601.39440-683633

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8515337 72.5
REV1315 6.2
010000565 2.7
F81503 2.4
TRN93502 2.4
0123455273 1.3
010232215 1.0
012012137 0.6
0112304567120 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-109153 43.3
10-20909 4.3
20-30801 3.8
30-40656 3.1
40-50519 2.5
50-60413 2.0
60-70361 1.7
70-80378 1.8
80-90293 1.4
90-100327 1.5
> 1007339 34.7

PARRIS

PARRIS usage summary as of Wed Sep 30 00:01:10 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14393939-39874874874-874959595-95
Last 30 days12 0.40 27.67 27.5021-39 589.75462286-1384 61.08 53.5020-135
Lifetime (4809 days)14568 3.03 20.11153-75 489.003297-11903 425.51 136.501-48648

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858241 56.6
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
0-0.12664 18.3
0.1-0.2517 3.5
0.2-0.3474 3.3
0.3-0.4370 2.5
0.4-0.5331 2.3
0.5-0.6392 2.7
0.6-0.7373 2.6
0.7-0.8359 2.5
0.8-0.9355 2.4
0.9-18733 59.9

GA Branch

GABranch usage summary as of Wed Sep 30 00:01:12 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14262626-26236236236-236232723272327-2327
Last 30 days11 0.37 26.452626-27 847.82434236-1384 3628.1831351951-7054
Lifetime (4802 days)11836 2.46 13.74123-30 520.973339-11628 5642.9615141-889396

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858563 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
34008 33.9
42224 18.8
5778 6.6
6237 2.0
7118 1.0
839 0.3
925 0.2

CMS

CMS usage summary as of Wed Sep 30 00:01:14 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days2 0.07 21.50 21.5018-25 413.50 413.50267-560436443641027-7701
Lifetime (3893 days)3272 0.84 33.71243-120 568.323447-1127621103.92 4037.5059-3262277

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
50-60180 5.5
60-70177 5.4
70-80129 3.9
80-90177 5.4
90-100111 3.4
> 1001496 45.7
Number of rate classesTimes found% found
10 0.0
22055 62.8
3718 21.9
4279 8.5
5118 3.6
650 1.5
715 0.5
82 0.1
91 0.0
≥ 1034 1.0

DEPS

DEPS usage summary as of Wed Sep 30 00:01:15 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days1 0.03303030-30269269269-269696969-69
Lifetime (3772 days)3570 0.95 35.84323-100 730.43 528.509-11100 488.88 145.502-31585

Subtyping

SCUEAL usage summary as of Wed Sep 30 00:01:17 2020 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days69716971.00 91.3540-500
Last 7 days6971995.86 91.3540-500
Last 30 days6971232.37 91.3540-500
Lifetime (4107 days)8275 2.01 94.5750-500

Top 10 Subtypes (out of 782606 sequences)

SubtypesTimes found% found
B310178 39.6
C151094 19.3
G51076 6.5
A145978 5.9
Complex32127 4.1
AE20674 2.6
D19648 2.5
CRF1412892 1.6
F112297 1.6
B,C recombinant9649 1.2

Coevolution

BGM usage summary as of Wed Sep 30 00:01:19 2020 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (2701 days)8881 3.29 65.10300-1033 2.25 0.98 0.01-263 2866.47920-2900666

UCSD Viral Evolution Group 2004-2020