Analyze your data Home Help Citations Job Queue Stats HyPhy package
Navigation Banner

SLAC

SLAC usage summary as of Tue Jul 27 00:00:01 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3901 days)92479 23.71 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 27 00:00:13 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days8 1.14 85.508635-188 316.6221176-985 618.50430128-1454
Last 30 days30 1.00 68.67 38.503-258 520.9350764-1248 795.20 691.5082-2225
Lifetime (3001 days)103997 34.65 44.59243-787 488.093251-11276 182.65460-51470

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8547282 45.5
REV13370 12.9
TRN9310158 9.8
F815438 5.2
0100003929 3.8
0102322094 2.0
0120121583 1.5
0122121405 1.4
0102301270 1.2
0120321005 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.084082 80.9
0.05 0.9 19.115388 14.8
0.2 2.1 29.72137 2.1
0.25 3.1 31.9942 0.9
0.01 0.4 14.6524 0.5
0.5 5.9 43.2214 0.2
0.15 2.2 22.9182 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 27 00:00:26 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14353535-35344344344-344162162162-162
Last 30 days44 1.47 25.73243-62 677.27739181-920 177.66 168.5013-484
Lifetime (3000 days)58285 19.43 20.71162-110 488.353231-11542 389.411110-54132

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8531013 53.2
REV5721 9.8
F813547 6.1
TRN933373 5.8
0100002345 4.0
0120121239 2.1
001101730 1.3
012212720 1.2
010232709 1.2
012032623 1.1
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.852679 90.4
100 4.4 22.11322 2.3
90 19.2 11.2901 1.5
20 7.2 36.0826 1.4
95 2.4 31.6783 1.3
10 5.8 31.7750 1.3
40 2.5 24.4145 0.2
25 7.8 34.7115 0.2
80 3.0 28.9111 0.2
30 9.8 20.693 0.2

TOGGLE

Toggle usage summary as of Tue Jul 27 00:00:33 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (4081 days)1092 0.27 47.53377-150 568.7335016-3789 3765.88 1970.5031-42841

Model Select.

ModelSelection usage summary as of Tue Jul 27 00:00:35 2021 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days4 0.57 66.256642-91 76.75 76.5076-78
Last 30 days49 1.6333273-109 592.2073924-1248
Lifetime (3001 days)102687 34.22 43.79223-656 523.103251-11935

Top 10 Models

ModelTimes selected% selected
HKY8524656 24.0
TRN9313107 12.8
F818966 8.7
0102324383 4.3
0120123612 3.5
0122123102 3.0
0102302487 2.4
0120322439 2.4
0122322437 2.4
0011012116 2.1

Protein Model Select.

ModelSelectionP usage summary as of Tue Jul 27 00:00:44 2021 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days10 10.00 71.20 88.507-92 9768.2098059510-9935
Last 7 days17 2.43 63.06887-92 9736.7198059510-9935
Last 30 days29 0.97 73.07767-441 9135.979805111-10018
Lifetime (4802 days)4001 0.83 46.65262-500 794.344513-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F567 14.2
JTT (Jones,Taylor,Thornton)410 10.2
BLOSUM62+F328 8.2
WAG (Whelan and Goldman)+F326 8.1
HIV (within host)+F295 7.4
IAV (Influenza A virus)+F266 6.6
WAG (Whelan and Goldman)245 6.1
IAV (Influenza A virus)228 5.7
BLOSUM62169 4.2
HIV (between hosts)+F169 4.2

GARD

GARD usage summary as of Tue Jul 27 00:00:46 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days5 0.71 98.8010842-188 1542.601344228-2955 2022.402267255-3708
Last 30 days18 0.60 42.83 21.503-188 2536.17295572-4896 1677.06 1224.5034-4041
Lifetime (5354 days)76200 14.23 26.94182-300 2045.39111620-46625 1292.513861-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
064511 84.7
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
0-1027732 36.4
10-203031 4.0
20-302445 3.2
30-402276 3.0
40-501871 2.5
50-601977 2.6
60-701454 1.9
70-801325 1.7
80-901227 1.6
90-1001088 1.4
> 10031774 41.7
Number of breakpointsTimes found% found
023350 30.6
119260 25.3
212087 15.9
37034 9.2
44283 5.6
52947 3.9
61903 2.5
71419 1.9
8940 1.2
9762 1.0
≥ 102215 2.9

SBP

SBP usage summary as of Tue Jul 27 00:00:56 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29121212-12111-1420420381-459
Last 30 days9 0.30 65.56125-336 28.8911-121 1430.673819-9801
Lifetime (3001 days)21286 7.09 50.41252-656 21.7811-45015 623.75440-683633

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8515438 72.5
REV1315 6.2
010000565 2.7
F81503 2.4
TRN93502 2.4
0123455293 1.4
010232215 1.0
012012137 0.6
0112304567125 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-109206 43.2
10-20916 4.3
20-30805 3.8
30-40658 3.1
40-50520 2.4
50-60416 2.0
60-70361 1.7
70-80379 1.8
80-90293 1.4
90-100329 1.5
> 1007403 34.8

PARRIS

PARRIS usage summary as of Tue Jul 27 00:01:00 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (5109 days)14607 2.86 20.12153-75 489.633297-11903 425.561361-48648

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858268 56.6
F811080 7.4
REV1011 6.9
TRN93777 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
0-0.12668 18.3
0.1-0.2518 3.5
0.2-0.3476 3.3
0.3-0.4373 2.6
0.4-0.5331 2.3
0.5-0.6393 2.7
0.6-0.7373 2.6
0.7-0.8360 2.5
0.8-0.9355 2.4
0.9-18760 60.0

GA Branch

GABranch usage summary as of Tue Jul 27 00:01:02 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (5102 days)11882 2.33 13.75123-30 522.523339-11628 5654.0415191-889396

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858609 72.5
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
24315 36.3
34022 33.8
42241 18.9
5780 6.6
6238 2.0
7119 1.0
840 0.3
928 0.2

CMS

CMS usage summary as of Tue Jul 27 00:01:04 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14131313-13183418341834-1834627862786278-6278
Last 30 days5 0.17 20.20229-33 671.20544156-1834 6587.606278445-17622
Lifetime (4193 days)3316 0.79 33.64243-120 572.333487-1127621139.47406059-3262277

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10193 5.8
10-20152 4.6
20-30194 5.9
30-40223 6.7
40-50249 7.5
50-60184 5.5
60-70178 5.4
70-80129 3.9
80-90178 5.4
90-100111 3.3
> 1001525 46.0
Number of rate classesTimes found% found
10 0.0
22075 62.6
3728 22.0
4284 8.6
5123 3.7
653 1.6
716 0.5
82 0.1
91 0.0
≥ 1034 1.0

DEPS

DEPS usage summary as of Tue Jul 27 00:01:05 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days13 13.00 75.31897-92 9776.6998059510-9935 391.0845433-540
Last 7 days19 2.71 65.79887-92 9743.8998059510-9935 321.5837424-540
Last 30 days27 0.90 57.85817-92 9797.0498059510-10018 301.3331924-1113
Lifetime (4072 days)3642 0.89 35.92313-100 890.965409-11100 484.121442-31585

Subtyping

SCUEAL usage summary as of Tue Jul 27 00:01:07 2021 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days71227122.00 90.5440-500
Last 7 days71221017.43 90.5440-500
Last 30 days7122237.40 90.5440-500
Lifetime (4407 days)8426 1.91 93.8450-500

Top 10 Subtypes (out of 790686 sequences)

SubtypesTimes found% found
B312432 39.5
C152608 19.3
G51613 6.5
A146710 5.9
Complex33039 4.2
AE20785 2.6
D19758 2.5
CRF1412918 1.6
F112537 1.6
B,C recombinant9834 1.2

Coevolution

BGM usage summary as of Tue Jul 27 00:01:10 2021 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3001 days)8881 2.96 65.10300-1033 2.25 0.98 0.01-263 2866.47920-2900666

UCSD Viral Evolution Group 2004-2021