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SLAC

SLAC usage summary as of Sat Nov 26 00:00:03 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (4388 days)92479 21.08 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 Sat Nov 26 00:00:15 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3488 days)104431 29.94 44.59243-787 488.423251-11276 182.27460-51470

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8547603 45.6
REV13414 12.8
TRN9310164 9.7
F815467 5.2
0100003929 3.8
0102322094 2.0
0120121584 1.5
0122121406 1.3
0102301270 1.2
0120321005 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 23.984473 80.9
0.05 0.9 19.115415 14.8
0.2 2.1 29.72137 2.0
0.25 3.1 31.9942 0.9
0.01 0.5 15.1530 0.5
0.5 6.0 43.1215 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 Sat Nov 26 00:00:28 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3487 days)58372 16.74 20.71162-110 488.513231-11542 389.041110-54132

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8531083 53.2
REV5725 9.8
F813554 6.1
TRN933376 5.8
0100002345 4.0
0120121240 2.1
001101730 1.3
012212720 1.2
010232709 1.2
012032623 1.1
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.852765 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 31.6784 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 Sat Nov 26 00:00:35 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (4568 days)1095 0.24 47.56377-150 567.7435016-3789 3755.66196627-42841

Model Select.

ModelSelection usage summary as of Sat Nov 26 00:00:37 2022 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3488 days)103015 29.53 43.82223-656 523.503251-11935

Top 10 Models

ModelTimes selected% selected
HKY8524737 24.0
TRN9313124 12.7
F819029 8.8
0102324394 4.3
0120123621 3.5
0122123103 3.0
0102302487 2.4
0120322461 2.4
0122322439 2.4
0011012123 2.1

Protein Model Select.

ModelSelectionP usage summary as of Sat Nov 26 00:00:46 2022 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (5289 days)4241 0.80 46.17262-500 1067.064703-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F570 13.4
JTT (Jones,Taylor,Thornton)412 9.7
HIV (within host)+F412 9.7
BLOSUM62+F341 8.0
WAG (Whelan and Goldman)+F341 8.0
IAV (Influenza A virus)+F337 7.9
WAG (Whelan and Goldman)245 5.8
IAV (Influenza A virus)228 5.4
HIV (between hosts)+F180 4.2
BLOSUM62170 4.0

GARD

GARD usage summary as of Sat Nov 26 00:00:48 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days2 2.00222222-22769769769-769 88.50 88.5087-90
Last 7 days3 0.43 21.332220-22 879.33769769-11001069087-141
Last 30 days6 0.20422218-85 738.50737544-1100 282.67 115.5022-680
Lifetime (5841 days)76452 13.09 26.96182-300 2046.28111620-46625 1291.043861-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
064763 84.7
HKY855991 7.8
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
0-1027885 36.5
10-203043 4.0
20-302447 3.2
30-402279 3.0
40-501877 2.5
50-601980 2.6
60-701459 1.9
70-801325 1.7
80-901228 1.6
90-1001090 1.4
> 10031839 41.6
Number of breakpointsTimes found% found
023465 30.7
119353 25.3
212108 15.8
37046 9.2
44289 5.6
52949 3.9
61904 2.5
71419 1.9
8940 1.2
9764 1.0
≥ 102215 2.9

SBP

SBP usage summary as of Sat Nov 26 00:00:57 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days6 0.20555018-143 6.6771-11 662.17 500.501-2446
Lifetime (3488 days)21477 6.16 50.78252-656 21.7211-45015 699.12450-683633

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8515583 72.6
REV1315 6.1
010000565 2.6
F81503 2.3
TRN93502 2.3
0123455326 1.5
010232215 1.0
012012137 0.6
0112304567128 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-109276 43.2
10-20919 4.3
20-30809 3.8
30-40658 3.1
40-50528 2.5
50-60417 1.9
60-70364 1.7
70-80380 1.8
80-90295 1.4
90-100329 1.5
> 1007502 34.9

PARRIS

PARRIS usage summary as of Sat Nov 26 00:01:01 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (5596 days)14661 2.62 20.08153-75 491.593297-11903 424.601361-48648

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858319 56.7
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
0-0.12673 18.2
0.1-0.2518 3.5
0.2-0.3478 3.3
0.3-0.4373 2.5
0.4-0.5332 2.3
0.5-0.6393 2.7
0.6-0.7374 2.6
0.7-0.8361 2.5
0.8-0.9355 2.4
0.9-18804 60.1

GA Branch

GABranch usage summary as of Sat Nov 26 00:01:03 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (5589 days)11904 2.13 13.75123-30 522.343339-11628 5647.3715161-889396

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858631 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
24323 36.3
34028 33.8
42245 18.9
5783 6.6
6239 2.0
7119 1.0
840 0.3
928 0.2

CMS

CMS usage summary as of Sat Nov 26 00:01:05 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (4680 days)3439 0.73 33.10243-120 574.973527-1127620640.63404359-3262277

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10193 5.6
10-20152 4.4
20-30199 5.8
30-40234 6.8
40-50256 7.4
50-60184 5.4
60-70180 5.2
70-80133 3.9
80-90181 5.3
90-100112 3.3
> 1001615 47.0
Number of rate classesTimes found% found
10 0.0
22122 61.7
3753 21.9
4315 9.2
5139 4.0
656 1.6
717 0.5
82 0.1
91 0.0
≥ 1034 1.0

DEPS

DEPS usage summary as of Sat Nov 26 00:01:06 2022 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (4559 days)3766 0.83 35.79313-100 1082.485569-11100 473.301412-31585

Subtyping

SCUEAL usage summary as of Sat Nov 26 00:01:08 2022 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days73767376.00 88.4040-500
Last 7 days73761053.71 88.4040-500
Last 30 days7376245.87 88.4040-500
Lifetime (4894 days)8680 1.77 91.9250-500

Top 10 Subtypes (out of 797859 sequences)

SubtypesTimes found% found
B314265 39.4
C153099 19.2
G52864 6.6
A147172 5.9
Complex33834 4.2
AE20841 2.6
D19948 2.5
CRF1412971 1.6
F112729 1.6
B,C recombinant9957 1.2

Coevolution

BGM usage summary as of Sat Nov 26 00:01:10 2022 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3488 days)8881 2.55 65.10300-1033 2.25 0.98 0.01-263 2866.47920-2900666

UCSD Viral Evolution Group 2004-2022