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SLAC

SLAC usage summary as of Sun Apr 22 00:00:03 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days3 3.001296-21 121.677562-228 0.80 0.60 0.53- 1.28
Last 7 days223 31.86 51.09273-402 464.8032635-2334 10.24 3.78 0.22- 161.09
Last 30 days798 26.60 51.97353-421 484.0632519-4249 11.72 4.54 0.22- 265.82
Lifetime (2709 days)86970 32.10 51.99253-684 487.373251-11903 21.56 6.24 0.16- 7571.98

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8545044 51.8
TRN9312804 14.7
REV9261 10.6
F813836 4.4
010230985 1.1
010232976 1.1
012212920 1.1
012012841 1.0
012232743 0.9
010000660 0.8
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 0.6 16.272903 83.8
0.05 0.5 14.510581 12.2
0.2 0.9 17.31251 1.4
0.25 2.3 25.7723 0.8
0.5 4.4 55.2561 0.6
0.01 0.8 9.4521 0.6
0.15 2.9 14.888 0.1
0.0024 0.0 2.345 0.1
0.3 0.2 20.045 0.1
0.0048 0.0 0.533 0.0

FEL

FEL usage summary as of Sun Apr 22 00:00:15 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days2 2.00 13.50 13.506-21 68.50 68.5062-75995-13
Last 7 days97 13.86 38.13214-369 381.7430951-2334 51.99335-433
Last 30 days578 19.27 33.45143-377 500.7627319-3801 68.15261-3013
Lifetime (1809 days)97403 53.84 44.21243-787 478.623251-11276 141.06440-26278

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8543870 45.0
REV12874 13.2
TRN939551 9.8
F814792 4.9
0100003917 4.0
0102322021 2.1
0120121402 1.4
0122121305 1.3
0102301189 1.2
012032926 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.278942 81.0
0.05 0.9 19.314468 14.9
0.2 2.2 29.11877 1.9
0.25 3.2 33.4845 0.9
0.01 0.4 14.3484 0.5
0.5 5.6 44.7187 0.2
0.15 2.9 21.9131 0.1
0.0024 0.0 7.0102 0.1
0.3 1.2 22.363 0.1
0.0004 0.0 6.629 0.0

REL

REL usage summary as of Sun Apr 22 00:00:28 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days3 3.001166-21 70.677562-75 50.333837-76
Last 7 days37 5.29 15.30125-53 546.0529151-2334 341.35908-6351
Last 30 days296 9.87 25.35154-75 494.0824719-3801 327.36 88.502-11181
Lifetime (1808 days)54380 30.08 20.60162-110 481.003181-10798 363.051080-39109

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8528809 53.0
REV5573 10.2
TRN933163 5.8
F813098 5.7
0100002329 4.3
0120121040 1.9
001101714 1.3
010232683 1.3
012212659 1.2
012032554 1.0
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.749105 90.3
100 4.2 22.61283 2.4
90 19.4 11.1890 1.6
20 7.3 36.2807 1.5
10 5.8 31.9728 1.3
95 2.3 28.0642 1.2
40 2.5 24.5144 0.3
80 3.1 28.0103 0.2
30 10.2 20.689 0.2
25 2.5 38.279 0.1

TOGGLE

Toggle usage summary as of Sun Apr 22 00:00:34 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29161616-16326326326-326604604431-777
Last 30 days3 0.10 14.671612-16 880.33326326-1989 689.67777431-861
Lifetime (2889 days)1040 0.36 48.36397-150 570.6234616-3789 3832.52 2012.5031-42841

Model Select.

ModelSelection usage summary as of Sun Apr 22 00:00:35 2018 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days3 3.00 112.671649-165 426.33525228-526
Last 7 days196 28.00 58.57353-428 390.8330951-2334
Last 30 days766 25.53 49.45263-428 524.5035919-3800
Lifetime (1809 days)94493 52.23 41.55223-656 515.403251-11935

Top 10 Models

ModelTimes selected% selected
HKY8522713 24.0
TRN9312401 13.1
F818324 8.8
0102324182 4.4
0120123077 3.3
0122122796 3.0
0102302236 2.4
0120322159 2.3
0122322116 2.2
0011011986 2.1

Protein Model Select.

ModelSelectionP usage summary as of Sun Apr 22 00:00:44 2018 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days1 1.00888-8228228228-228
Last 7 days2 0.292172178-426334334228-440
Last 30 days10 0.33 124.10 87.508-426 1301.70643228-3551
Lifetime (3610 days)3726 1.03 45.76252-499 646.424443-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F547 14.7
JTT (Jones,Taylor,Thornton)399 10.7
BLOSUM62+F310 8.3
WAG (Whelan and Goldman)+F307 8.2
WAG (Whelan and Goldman)240 6.4
IAV (Influenza A virus)+F235 6.3
HIV (within host)+F230 6.2
IAV (Influenza A virus)215 5.8
BLOSUM62163 4.4
LG (Le and Gascuel)149 4.0

GARD

GARD usage summary as of Sun Apr 22 00:00:46 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00164164164-164157515751575-1575243324332433-2433
Last 7 days44 6.29 31.77153-211 1631.681773210-3450 1579.73 828.5068-3954
Last 30 days177 5.90 31.34173-211 1955.791185156-10653 1321.3057636-4731
Lifetime (4162 days)73591 17.68 26.82182-300 2030.66111220-46625 1270.383741-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
061902 84.1
HKY855991 8.1
010000860 1.2
REV830 1.1
TRN93558 0.8
F81520 0.7
010232226 0.3
012212218 0.3
010230182 0.2
012232144 0.2
delta AIC rangeTimes found% found
0-1026685 36.3
10-202934 4.0
20-302359 3.2
30-402203 3.0
40-501808 2.5
50-601934 2.6
60-701395 1.9
70-801295 1.8
80-901192 1.6
90-1001064 1.4
> 10030722 41.7
Number of breakpointsTimes found% found
022416 30.5
118652 25.3
211664 15.8
36761 9.2
44102 5.6
52841 3.9
61849 2.5
71400 1.9
8932 1.3
9759 1.0
≥ 102215 3.0

SBP

SBP usage summary as of Sun Apr 22 00:00:55 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days12 1.71 102.255310-377 7.7521-54 294.08 67.501-1777
Last 30 days53 1.77 66.96376-500 127.4931-1259 460.02841-4406
Lifetime (1809 days)20142 11.13 48.53242-656 21.7811-45015 473.32410-279793

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8514442 71.7
REV1311 6.5
010000565 2.8
TRN93500 2.5
F81500 2.5
0123455224 1.1
010232215 1.1
012012137 0.7
0112304567114 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-108697 43.2
10-20886 4.4
20-30763 3.8
30-40617 3.1
40-50501 2.5
50-60401 2.0
60-70350 1.7
70-80368 1.8
80-90278 1.4
90-100300 1.5
> 1006981 34.7

PARRIS

PARRIS usage summary as of Sun Apr 22 00:00:58 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days118 3.93 7.9764-48 478.9750499-909 57.2981-797
Lifetime (3917 days)14142 3.61 20.19153-75 484.223287-11903 414.971371-35284

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY857979 56.4
F811051 7.4
REV995 7.0
TRN93736 5.2
010000429 3.0
012012250 1.8
001101166 1.2
012212153 1.1
012032127 0.9
010230119 0.8
p-values rangeTimes found% found
0-0.12597 18.4
0.1-0.2502 3.5
0.2-0.3456 3.2
0.3-0.4359 2.5
0.4-0.5325 2.3
0.5-0.6386 2.7
0.6-0.7363 2.6
0.7-0.8349 2.5
0.8-0.9344 2.4
0.9-18461 59.8

GA Branch

GABranch usage summary as of Sun Apr 22 00:01:00 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days3 0.43 10.3395-17 1238.671150232-2334 1740.67156715-3640
Last 30 days9 0.30 13.67115-26 821.2227030-2334 1790.67156715-6092
Lifetime (3910 days)11566 2.96 13.73123-30 514.753299-11628 5302.4215071-636439

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858299 71.8
REV613 5.3
010000568 4.9
F81414 3.6
TRN93281 2.4
012012131 1.1
001101107 0.9
01221264 0.6
01001263 0.5
00001060 0.5
the number of dN/dS classes rangeTimes found% found
199 0.9
24239 36.7
33913 33.8
42163 18.7
5756 6.5
6227 2.0
7111 1.0
835 0.3
923 0.2

CMS

CMS usage summary as of Sun Apr 22 00:01:02 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14414141-41511511511-511191251912519125-19125
Last 30 days8 0.2737 27.506-101 520.25 507.50209-706 7405.122333177-22833
Lifetime (3001 days)3075 1.02 33.85243-120 536.903347-1127617819.02391859-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10183 6.0
10-20141 4.6
20-30186 6.0
30-40212 6.9
40-50239 7.8
50-60173 5.6
60-70170 5.5
70-80126 4.1
80-90168 5.5
90-100107 3.5
> 1001370 44.6
Number of rate classesTimes found% found
10 0.0
21958 63.7
3669 21.8
4253 8.2
5100 3.3
645 1.5
714 0.5
82 0.1
90 0.0
≥ 1034 1.1

DEPS

DEPS usage summary as of Sun Apr 22 00:01:03 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days1 0.03101010-10233423342334-2334373737-37
Lifetime (2880 days)2716 0.94 32.00243-100 580.16 435.509-11100 435.711002-31585

Subtyping

SCUEAL usage summary as of Sun Apr 22 00:01:04 2018 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days57875787.00 82.3440-500
Last 7 days5787826.71 82.3440-500
Last 30 days5787192.90 82.3440-500
Lifetime (3215 days)7091 2.21 87.7650-500

Top 10 Subtypes (out of 622318 sequences)

SubtypesTimes found% found
B242050 38.9
C107314 17.2
G44715 7.2
A139575 6.4
Complex25730 4.1
AE17977 2.9
D17101 2.7
CRF1411644 1.9
F19752 1.6
B,C recombinant8093 1.3

Coevolution

BGM usage summary as of Sun Apr 22 00:01:06 2018 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days4 0.57 72.75 49.506-186 0.78 0.53 0.05-262 2.501-242
Last 30 days7 0.23 75.71566-186 1.45 0.88 0.05- 4.93 681.4361-4286
Lifetime (1809 days)8697 4.81 64.75300-1033 2.26 0.98 0.01-263 2917.15960-2900666

UCSD Viral Evolution Group 2004-2018