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SLAC

SLAC usage summary as of Sun Dec 8 00:00:01 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3304 days)92479 27.99 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 Sun Dec 8 00:00:13 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days17 2.43 59.41483-251 201.418076-973 692.59370242-4157
Last 30 days80 2.67 51.42303-327 575.6032576-3443 2070.03 924.50190-14824
Lifetime (2404 days)102396 42.59 44.32243-787 484.143251-11276 156.62450-51470

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8546335 45.3
REV13224 12.9
TRN9310067 9.8
F815269 5.1
0100003926 3.8
0102322082 2.0
0120121581 1.5
0122121386 1.4
0102301254 1.2
012032996 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.182813 80.9
0.05 0.9 19.115141 14.8
0.2 2.1 29.82118 2.1
0.25 3.1 32.5909 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 Sun Dec 8 00:00:27 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00666-6898989-89124124124-124
Last 7 days39 5.57 16.49103-74 229.088945-909 185.5612323-962
Last 30 days54 1.80 18.89153-74 279.09 169.5045-909 512.35 134.5023-4566
Lifetime (2403 days)57060 23.75 20.68162-110 485.223231-10798 389.141100-54132

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8530271 53.1
REV5668 9.9
F813386 5.9
TRN933336 5.8
0100002339 4.1
0120121202 2.1
001101728 1.3
012212704 1.2
010232694 1.2
012032614 1.1
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.951622 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 30.9715 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 Sun Dec 8 00:00:33 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days1 0.03222222-22103210321032-1032483483483-483
Lifetime (3484 days)1080 0.31 47.61377-150 571.6535016-3789 3784.18 1970.5031-42841

Model Select.

ModelSelection usage summary as of Sun Dec 8 00:00:35 2019 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days2 2.00 86.50 86.506-167 496.50 496.5089-904
Last 7 days26 3.71 23.58113-167 256.588945-1053
Last 30 days131 4.37 29.48173-167 450.3735145-3434
Lifetime (2404 days)100904 41.97 43.67223-656 519.953251-11935

Top 10 Models

ModelTimes selected% selected
HKY8524237 24.0
TRN9312995 12.9
F818689 8.6
0102324314 4.3
0120123529 3.5
0122123044 3.0
0102302457 2.4
0120322401 2.4
0122322400 2.4
0011012096 2.1

Protein Model Select.

ModelSelectionP usage summary as of Sun Dec 8 00:00:44 2019 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (4205 days)3879 0.92 46.47252-500 652.084443-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F562 14.5
JTT (Jones,Taylor,Thornton)406 10.5
BLOSUM62+F326 8.4
WAG (Whelan and Goldman)+F321 8.3
HIV (within host)+F253 6.5
WAG (Whelan and Goldman)244 6.3
IAV (Influenza A virus)+F241 6.2
IAV (Influenza A virus)225 5.8
BLOSUM62168 4.3
LG (Le and Gascuel)162 4.2

GARD

GARD usage summary as of Sun Dec 8 00:00:46 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days4 4.00282828-28233823382338-2338 3535.7536263264-3627
Last 7 days7 1.00 30.43288-49 1452.142338228-2338 2237.573264314-3627
Last 30 days37 1.23 42.35397-143 3937.681683228-10341 1929.571623122-5934
Lifetime (4757 days)75313 15.83 26.87182-300 2036.84111620-46625 1288.743831-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
063624 84.5
HKY855991 8.0
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
0-1027346 36.3
10-202999 4.0
20-302428 3.2
30-402259 3.0
40-501854 2.5
50-601961 2.6
60-701436 1.9
70-801316 1.7
80-901219 1.6
90-1001083 1.4
> 10031412 41.7
Number of breakpointsTimes found% found
023006 30.5
119055 25.3
211948 15.9
36948 9.2
44240 5.6
52910 3.9
61882 2.5
71413 1.9
8935 1.2
9761 1.0
≥ 102215 2.9

SBP

SBP usage summary as of Sun Dec 8 00:00:56 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days6 6.00 26.502819-28111-1 525.67 607.5085-636
Last 7 days6 0.86 26.502819-28111-1 525.67 607.5085-636
Last 30 days47 1.57 23.06153-197 12.4711-369 255.361872-1718
Lifetime (2404 days)20850 8.67 49.81252-656 21.7711-45015 597.11420-683633

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8515094 72.4
REV1315 6.3
010000565 2.7
F81503 2.4
TRN93502 2.4
0123455246 1.2
010232215 1.0
012012137 0.7
0112304567119 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-109030 43.3
10-20899 4.3
20-30796 3.8
30-40648 3.1
40-50511 2.5
50-60410 2.0
60-70359 1.7
70-80376 1.8
80-90285 1.4
90-100319 1.5
> 1007217 34.6

PARRIS

PARRIS usage summary as of Sun Dec 8 00:00:59 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days3 0.43202020-20921921921-921 91.339289-93
Last 30 days14 0.47 20.93 21.5016-24 966.86958829-1079 217.9318989-494
Lifetime (4512 days)14443 3.20 20.13153-75 486.473297-11903 426.551371-48648

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858174 56.6
F811068 7.4
REV1008 7.0
TRN93758 5.2
010000429 3.0
012012259 1.8
001101166 1.1
012212155 1.1
012032132 0.9
010230125 0.9
p-values rangeTimes found% found
0-0.12634 18.2
0.1-0.2514 3.6
0.2-0.3465 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 2.5
0.9-18660 60.0

GA Branch

GABranch usage summary as of Sun Dec 8 00:01:01 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14191919-19105310531053-1053198141981419814-19814
Last 30 days1 0.03191919-19105310531053-1053198141981419814-19814
Lifetime (4505 days)11730 2.60 13.73123-30 520.003329-11628 5664.2915211-889396

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858457 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
33958 33.7
42199 18.7
5774 6.6
6234 2.0
7118 1.0
838 0.3
925 0.2

CMS

CMS usage summary as of Sun Dec 8 00:01:03 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.2917178-26117117116-118 1079.50 1079.50910-1249
Last 30 days2 0.0717178-26117117116-118 1079.50 1079.50910-1249
Lifetime (3596 days)3208 0.89 33.70243-120 563.643407-1127621203.02 4066.5059-3262277

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10184 5.7
10-20147 4.6
20-30189 5.9
30-40217 6.8
40-50243 7.6
50-60179 5.6
60-70174 5.4
70-80129 4.0
80-90175 5.5
90-100108 3.4
> 1001463 45.6
Number of rate classesTimes found% found
10 0.0
22017 62.9
3707 22.0
4272 8.5
5112 3.5
648 1.5
715 0.5
82 0.1
91 0.0
≥ 1034 1.1

DEPS

DEPS usage summary as of Sun Dec 8 00:01:04 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14808080-80161161161-161587587587-587
Last 30 days1 0.03808080-80161161161-161587587587-587
Lifetime (3475 days)3407 0.98 35.24303-100 653.055019-11100 500.891402-31585

Subtyping

SCUEAL usage summary as of Sun Dec 8 00:01:06 2019 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days64366436.00 81.5930-500
Last 7 days6436919.43 81.5930-500
Last 30 days6436214.53 81.5930-500
Lifetime (3810 days)7740 2.03 86.6950-500

Top 10 Subtypes (out of 670946 sequences)

SubtypesTimes found% found
B261162 38.9
C117176 17.5
G46069 6.9
A142088 6.3
Complex28207 4.2
AE19814 3.0
D18959 2.8
CRF1411763 1.8
F110613 1.6
B,C recombinant9164 1.4

Coevolution

BGM usage summary as of Sun Dec 8 00:01:08 2019 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (2404 days)8881 3.69 65.10300-1033 2.25 0.98 0.01-263 2866.47920-2900666

UCSD Viral Evolution Group 2004-2019