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SLAC

SLAC usage summary as of Wed Apr 24 00:00:02 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days266 8.87 146.10903-492 594.85 467.5060-3958 39.68 17.88 0.26- 191.60
Lifetime (3076 days)92479 30.06 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 Apr 24 00:00:14 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00555-5461461461-461301301301-301
Last 7 days32 4.575494-278 668.12738174-2036 714.81 440.50110-3671
Last 30 days282 9.40 40.54233-297 678.9046041-3958 1156.15 324.505-14810
Lifetime (2176 days)101334 46.57 44.23243-787 483.173251-11276 148.26450-26278

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8545657 45.1
REV13160 13.0
TRN939984 9.9
F815215 5.1
0100003926 3.9
0102322074 2.0
0120121557 1.5
0122121372 1.4
0102301228 1.2
012032989 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.181940 80.9
0.05 0.9 19.215005 14.8
0.2 2.1 30.02069 2.0
0.25 3.1 32.5909 0.9
0.01 0.4 14.7520 0.5
0.5 5.9 42.7212 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 Wed Apr 24 00:00:28 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00555-5461461461-461636363-63
Last 7 days34 4.86 13.3854-58 795.65742174-2321 218.15 66.5015-1196
Last 30 days118 3.93 20.26153-75 722.07 588.506-3392 1895.56 270.5012-40807
Lifetime (2175 days)56296 25.88 20.63162-110 485.263221-10798 381.211090-54132

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8529759 52.9
REV5632 10.0
F813319 5.9
TRN933315 5.9
0100002336 4.1
0120121182 2.1
001101727 1.3
012212699 1.2
010232694 1.2
012032603 1.1
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.850884 90.4
100 4.3 22.51297 2.3
90 19.2 11.2900 1.6
20 7.2 36.0819 1.5
10 5.8 31.7744 1.3
95 2.2 30.7700 1.2
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 Wed Apr 24 00:00:34 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days2 0.07636324-102207207201-21317480.5017480.502781-32180
Lifetime (3256 days)1075 0.33 47.54377-150 568.8135016-3789 3782.81196831-42841

Model Select.

ModelSelection usage summary as of Wed Apr 24 00:00:35 2019 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days12 12.00 52.2587-461 342.8323397-758
Last 7 days38 5.43 36.82 20.504-461 514.3227397-2036
Last 30 days325 10.83 143.19873-499 603.584986-3392
Lifetime (2176 days)99483 45.72 43.04223-656 518.323251-11935

Top 10 Models

ModelTimes selected% selected
HKY8523932 24.1
TRN9312888 13.0
F818625 8.7
0102324295 4.3
0120123432 3.4
0122122982 3.0
0102302381 2.4
0122322358 2.4
0120322355 2.4
0011012083 2.1

Protein Model Select.

ModelSelectionP usage summary as of Wed Apr 24 00:00:44 2019 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days2 2.00555510-100976976233-1719
Last 7 days2 0.29555510-100976976233-1719
Last 30 days9 0.30 87.335710-223 416.33216210-1719
Lifetime (3977 days)3835 0.96 46.10252-499 651.044443-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F559 14.6
JTT (Jones,Taylor,Thornton)404 10.5
BLOSUM62+F324 8.4
WAG (Whelan and Goldman)+F319 8.3
WAG (Whelan and Goldman)244 6.4
HIV (within host)+F241 6.3
IAV (Influenza A virus)+F238 6.2
IAV (Influenza A virus)223 5.8
BLOSUM62167 4.4
LG (Le and Gascuel)161 4.2

GARD

GARD usage summary as of Wed Apr 24 00:00:46 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days32 1.07 46.19193-139 1639.50 1558.50348-5922 2562.662709138-7560
Lifetime (4529 days)74794 16.51 26.85182-300 2033.26111320-46625 1281.003781-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
063105 84.4
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
0-1027168 36.3
10-202988 4.0
20-302412 3.2
30-402239 3.0
40-501845 2.5
50-601949 2.6
60-701422 1.9
70-801312 1.8
80-901213 1.6
90-1001077 1.4
> 10031169 41.7
Number of breakpointsTimes found% found
022839 30.5
118951 25.3
211864 15.9
36880 9.2
44186 5.6
52888 3.9
61869 2.5
71407 1.9
8934 1.2
9761 1.0
≥ 102215 3.0

SBP

SBP usage summary as of Wed Apr 24 00:00:55 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days2 2.00373732-42111-1 423.50 423.50134-713
Last 7 days11 1.57 54.36409-201611-33 434.8221748-1661
Last 30 days58 1.93 157.05764-388 7.29 3.501-39 3421.74 1574.5010-21911
Lifetime (2176 days)20576 9.46 49.39242-656 21.7511-45015 566.95410-683633

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8514853 72.2
REV1315 6.4
010000565 2.7
F81503 2.4
TRN93502 2.4
0123455228 1.1
010232215 1.0
012012137 0.7
0112304567115 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-108900 43.3
10-20897 4.4
20-30788 3.8
30-40636 3.1
40-50508 2.5
50-60406 2.0
60-70353 1.7
70-80374 1.8
80-90282 1.4
90-100311 1.5
> 1007121 34.6

PARRIS

PARRIS usage summary as of Wed Apr 24 00:00:58 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days9 1.29 30.11404-58 518.22509174-1145 240.331967-844
Last 30 days66 2.20 13.4283-58 453.68 341.50116-1997 599.111517-14723
Lifetime (4284 days)14337 3.35 20.15153-75 486.273297-11903 424.221371-48648

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858119 56.6
F811064 7.4
REV1003 7.0
TRN93751 5.2
010000429 3.0
012012252 1.8
001101166 1.2
012212154 1.1
012032128 0.9
010230121 0.8
p-values rangeTimes found% found
0-0.12621 18.3
0.1-0.2510 3.6
0.2-0.3463 3.2
0.3-0.4363 2.5
0.4-0.5330 2.3
0.5-0.6389 2.7
0.6-0.7367 2.6
0.7-0.8357 2.5
0.8-0.9350 2.4
0.9-18587 59.9

GA Branch

GABranch usage summary as of Wed Apr 24 00:01:00 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29 6.50 6.504-9 507.50 507.50273-742106410648-2120
Last 30 days9 0.3015144-27 352.2233951-74212479.5621208-57340
Lifetime (4277 days)11702 2.74 13.73123-30 518.593319-11628 5559.51 1518.501-889396

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858431 72.0
REV614 5.2
010000568 4.9
F81415 3.5
TRN93283 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
24274 36.5
33953 33.8
42196 18.8
5771 6.6
6233 2.0
7116 1.0
836 0.3
924 0.2

CMS

CMS usage summary as of Wed Apr 24 00:01:02 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00999-9273273273-273250425042504-2504
Last 7 days5 0.71 19.2099-40 354.40273177-77621246.2035602504-51705
Last 30 days16 0.53 23.94 20.503-77 635.19 529.50177-335222322.5619351724-51705
Lifetime (3368 days)3174 0.94 33.69243-120 554.953407-1127618708.58401159-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10184 5.8
10-20146 4.6
20-30188 5.9
30-40215 6.8
40-50243 7.7
50-60178 5.6
60-70173 5.5
70-80127 4.0
80-90175 5.5
90-100108 3.4
> 1001437 45.3
Number of rate classesTimes found% found
10 0.0
22004 63.1
3700 22.1
4265 8.3
5107 3.4
648 1.5
714 0.4
82 0.1
90 0.0
≥ 1034 1.1

DEPS

DEPS usage summary as of Wed Apr 24 00:01:02 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days3 0.43 70.677459-79313378183-378438440308-566
Last 30 days8 0.27484610-79 246.12211183-378 362.62346193-566
Lifetime (3247 days)3119 0.96 34.18273-100 617.874819-11100 510.631262-31585

Subtyping

SCUEAL usage summary as of Wed Apr 24 00:01:03 2019 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days60936093.00 83.4440-500
Last 7 days6093870.43 83.4440-500
Last 30 days6093203.10 83.4440-500
Lifetime (3582 days)7397 2.07 88.4550-500

Top 10 Subtypes (out of 654241 sequences)

SubtypesTimes found% found
B257158 39.3
C111230 17.0
G45899 7.0
A141324 6.3
Complex26969 4.1
AE19222 2.9
D18758 2.9
CRF1411742 1.8
F110465 1.6
B,C recombinant8469 1.3

Coevolution

BGM usage summary as of Wed Apr 24 00:01:05 2019 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (2176 days)8881 4.08 65.10300-1033 2.25 0.98 0.01-263 2866.47920-2900666

UCSD Viral Evolution Group 2004-2019