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SLAC

SLAC usage summary as of Tue Jan 28 00:00:01 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3355 days)92479 27.56 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 Jan 28 00:00:13 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days4 4.00 189.25 183.5010-380 381.25 408.50142-56622381681892-4698
Last 7 days58 8.29 114.17426-488 552.4821042-3391 2855.57935279-22346
Last 30 days91 3.03 96.62414-488 535.0529742-3391 2616.781300248-22346
Lifetime (2455 days)102527 41.76 44.37243-787 484.223251-11276 159.58450-51470

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8546423 45.3
REV13237 12.9
TRN9310072 9.8
F815271 5.1
0100003928 3.8
0102322083 2.0
0120121581 1.5
0122121390 1.4
0102301256 1.2
012032996 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.182923 80.9
0.05 0.9 19.115156 14.8
0.2 2.1 29.82118 2.1
0.25 3.1 32.4915 0.9
0.01 0.4 14.7520 0.5
0.5 5.9 43.2214 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 Tue Jan 28 00:00:27 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days4 4.00 14.251311-20 430.7553189-572 898.50926124-1618
Last 7 days9 1.29 21.33159-49 325.4439276-572 669.22254124-1618
Last 30 days21 0.70 23.33195-52 462.6250376-1980 600.05375101-1618
Lifetime (2454 days)57125 23.28 20.68162-110 485.093231-10798 389.111110-54132

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8530307 53.1
REV5678 9.9
F813395 5.9
TRN933337 5.8
0100002341 4.1
0120121204 2.1
001101728 1.3
012212704 1.2
010232694 1.2
012032614 1.1
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.851685 90.5
100 4.3 22.41301 2.3
90 19.2 11.2900 1.6
20 7.2 35.9820 1.4
10 5.8 31.9747 1.3
95 2.2 30.9717 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 Tue Jan 28 00:00:33 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3535 days)1081 0.31 47.60377-150 571.6435016-3789 3781.73196831-42841

Model Select.

ModelSelection usage summary as of Tue Jan 28 00:00:35 2020 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days9 9.0096208-380 457.4425185-1983
Last 7 days45 6.43 173.71986-488 413.9321322-3391
Last 30 days87 2.90 117.17313-488 523.7851522-3391
Lifetime (2455 days)101065 41.17 43.73223-656 520.103251-11935

Top 10 Models

ModelTimes selected% selected
HKY8524263 24.0
TRN9313005 12.9
F818710 8.6
0102324328 4.3
0120123541 3.5
0122123049 3.0
0102302464 2.4
0120322409 2.4
0122322404 2.4
0011012096 2.1

Protein Model Select.

ModelSelectionP usage summary as of Tue Jan 28 00:00:44 2020 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days3 0.43939393-93566566566-566
Last 30 days9 0.30 69.229316-121 582.78566183-947
Lifetime (4256 days)3889 0.91 46.52252-500 651.814443-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F564 14.5
JTT (Jones,Taylor,Thornton)407 10.5
BLOSUM62+F326 8.4
WAG (Whelan and Goldman)+F321 8.3
HIV (within host)+F254 6.5
WAG (Whelan and Goldman)244 6.3
IAV (Influenza A virus)+F241 6.2
IAV (Influenza A virus)228 5.9
BLOSUM62169 4.3
LG (Le and Gascuel)163 4.2

GARD

GARD usage summary as of Tue Jan 28 00:00:46 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days7 1.00 50.864911-76 665.14639228-1593 674.71528379-1483
Last 30 days14 0.47 59.07 45.505-138 1710.64 1630.50228-5940 1712.79 932.50379-3805
Lifetime (4808 days)75365 15.67 26.89182-300 2036.76111620-46625 1289.053841-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
063676 84.5
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
0-1027372 36.3
10-203000 4.0
20-302428 3.2
30-402259 3.0
40-501854 2.5
50-601961 2.6
60-701436 1.9
70-801317 1.7
80-901219 1.6
90-1001083 1.4
> 10031436 41.7
Number of breakpointsTimes found% found
023031 30.6
119064 25.3
211952 15.9
36953 9.2
44243 5.6
52913 3.9
61885 2.5
71413 1.9
8935 1.2
9761 1.0
≥ 102215 2.9

SBP

SBP usage summary as of Tue Jan 28 00:00:55 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days15 2.1471766-267 25.3361-16646516716-2957
Last 30 days29 0.97 68.66766-267 15.0311-166 568.6241616-2957
Lifetime (2455 days)20886 8.51 49.85252-656 21.7711-45015 597.15420-683633

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8515125 72.4
REV1315 6.3
010000565 2.7
F81503 2.4
TRN93502 2.4
0123455248 1.2
010232215 1.0
012012137 0.7
0112304567119 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-109046 43.3
10-20901 4.3
20-30799 3.8
30-40648 3.1
40-50511 2.4
50-60410 2.0
60-70359 1.7
70-80376 1.8
80-90285 1.4
90-100320 1.5
> 1007231 34.6

PARRIS

PARRIS usage summary as of Tue Jan 28 00:00:59 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days4 0.13 23.502422-24 1179.2511411141-1294 463.25516232-589
Lifetime (4563 days)14462 3.17 20.13153-75 487.213297-11903 426.331371-48648

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858175 56.5
F811068 7.4
REV1008 7.0
TRN93758 5.2
010000429 3.0
012012262 1.8
001101166 1.1
012212155 1.1
012032137 0.9
010230125 0.9
p-values rangeTimes found% found
0-0.12645 18.3
0.1-0.2514 3.6
0.2-0.3466 3.2
0.3-0.4366 2.5
0.4-0.5331 2.3
0.5-0.6391 2.7
0.6-0.7370 2.6
0.7-0.8358 2.5
0.8-0.9354 2.4
0.9-18667 59.9

GA Branch

GABranch usage summary as of Tue Jan 28 00:01:01 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days5 0.17 22.602511-27 674.20684343-1029 7263.4066641237-13060
Lifetime (4556 days)11735 2.58 13.74123-30 520.073329-11628 5664.9715211-889396

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858462 72.1
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
24285 36.5
33961 33.8
42201 18.8
5774 6.6
6234 2.0
7118 1.0
838 0.3
925 0.2

CMS

CMS usage summary as of Tue Jan 28 00:01:03 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29 34.50 34.5026-43229229229-229492349233604-6242
Last 30 days16 0.53 45.38253-118 683.19758229-102923670.123124409-123741
Lifetime (3647 days)3230 0.89 33.79243-120 564.013417-1127621207.87406059-3262277

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10185 5.7
10-20149 4.6
20-30189 5.9
30-40217 6.7
40-50243 7.5
50-60179 5.5
60-70174 5.4
70-80129 4.0
80-90175 5.4
90-100111 3.4
> 1001479 45.8
Number of rate classesTimes found% found
10 0.0
22030 62.8
3708 21.9
4274 8.5
5116 3.6
650 1.5
715 0.5
82 0.1
91 0.0
≥ 1034 1.1

DEPS

DEPS usage summary as of Tue Jan 28 00:01:04 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29858577-93566566566-566 2223.50 2223.50673-3774
Last 30 days7 0.23 45.142620-93 629.71566183-947 932.4358570-3774
Lifetime (3526 days)3414 0.97 35.26303-100 653.00 503.509-11100 501.781402-31585

Subtyping

SCUEAL usage summary as of Tue Jan 28 00:01:05 2020 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days65196519.00 83.5140-500
Last 7 days6519931.29 83.5140-500
Last 30 days6519217.30 83.5140-500
Lifetime (3861 days)7823 2.03 88.2350-500

Top 10 Subtypes (out of 690213 sequences)

SubtypesTimes found% found
B261615 37.9
C134745 19.5
G46124 6.7
A142206 6.1
Complex28401 4.1
AE19846 2.9
D18998 2.8
CRF1411763 1.7
F110630 1.5
B,C recombinant9225 1.3

Coevolution

BGM usage summary as of Tue Jan 28 00:01:08 2020 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (2455 days)8881 3.62 65.10300-1033 2.25 0.98 0.01-263 2866.47920-2900666

UCSD Viral Evolution Group 2004-2020