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SLAC

SLAC usage summary as of Thu Sep 21 00:00:02 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days65 65.00 24.75124-143 427.5422631-3423 5.39 1.36 0.28- 107.94
Last 7 days346 49.43 32.61 17.504-295 455.03 278.5031-3956 6.30 2.04 0.23- 136.89
Last 30 days1156 38.53 36.29193-486 500.313256-7790 8.79 2.29 0.22- 1236.89
Lifetime (2496 days)81423 32.62 52.16253-684 482.333251-11903 22.17 6.33 0.16- 7571.98

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8542677 52.4
TRN9311941 14.7
REV8949 11.0
F813525 4.3
010232908 1.1
010230890 1.1
012212794 1.0
012012718 0.9
010000646 0.8
012232626 0.8
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 0.6 16.068202 83.8
0.05 0.6 14.69990 12.3
0.2 0.9 17.21169 1.4
0.25 2.3 25.1627 0.8
0.01 0.8 9.6508 0.6
0.5 4.4 54.6502 0.6
0.15 2.9 14.886 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 Thu Sep 21 00:00:12 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days34 34.00 12.03114-24 359.38 179.5055-1156 41.65 16.502-262
Last 7 days288 41.14 25.31164-295 443.75 278.5022-3956 69.94362-1009
Last 30 days729 24.30 32.03173-393 521.3132522-3956 105.05372-3379
Lifetime (1596 days)93381 58.51 43.94243-787 472.743251-10798 140.48440-26278

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8542235 45.2
REV12593 13.5
TRN939055 9.7
F814534 4.9
0100003897 4.2
0102321958 2.1
0120121309 1.4
0122121254 1.3
0102301110 1.2
001101884 0.9
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.075509 80.9
0.05 0.9 19.114063 15.1
0.2 2.1 28.51770 1.9
0.25 3.3 32.5784 0.8
0.01 0.4 14.6473 0.5
0.5 5.6 44.7187 0.2
0.15 2.9 21.7129 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 Thu Sep 21 00:00:24 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days32 32.00 11.47114-24 310.78 179.5055-1156 118.03 39.504-830
Last 7 days178 25.43 17.49154-62 460.5628046-3956 222.381093-3747
Last 30 days472 15.73 19.62163-73 508.5830022-3956 296.67 95.501-7163
Lifetime (1595 days)52296 32.79 20.44152-110 476.013161-10798 357.811070-38013

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8527845 53.2
REV5421 10.4
TRN932973 5.7
F812932 5.6
0100002323 4.4
012012977 1.9
001101684 1.3
010232663 1.3
012212620 1.2
012032491 0.9
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.447129 90.1
100 4.1 22.61269 2.4
90 19.6 10.9882 1.7
20 7.3 36.2782 1.5
10 5.8 31.8718 1.4
95 2.3 27.9612 1.2
40 2.5 24.5144 0.3
80 3.2 27.199 0.2
30 10.2 20.689 0.2
25 2.6 36.276 0.1

TOGGLE

Toggle usage summary as of Thu Sep 21 00:00:29 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00121212-12115611561156-1156107610761076-1076
Last 7 days1 0.14121212-12115611561156-1156107610761076-1076
Last 30 days7 0.23 44.862112-89 626.5725632-2095 3983.141076293-15030
Lifetime (2676 days)966 0.36 48.52397-150 570.9634416-3789 3942.63 2076.5031-42841

Model Select.

ModelSelection usage summary as of Thu Sep 21 00:00:31 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days48 48.00 24.42164-281 680.1235255-3722
Last 7 days285 40.71 30.54174-437 552.0430923-11709
Last 30 days827 27.57 37.15193-437 578.3132522-11709
Lifetime (1596 days)89229 55.91 41.25223-656 511.263251-11935

Top 10 Models

ModelTimes selected% selected
HKY8521483 24.1
TRN9311762 13.2
F818046 9.0
0102323988 4.5
0120122846 3.2
0122122610 2.9
0102302115 2.4
0122321897 2.1
0011011894 2.1
0120321888 2.1

Protein Model Select.

ModelSelectionP usage summary as of Thu Sep 21 00:00:39 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days1 1.00717171-71560856085608-5608
Last 7 days11 1.57 74.36826-147 2854.823434227-5608
Last 30 days35 1.17 119.29885-412 1581.5756643-5876
Lifetime (3397 days)3600 1.06 45.30 24.502-499 644.114443-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F531 14.8
JTT (Jones,Taylor,Thornton)391 10.9
BLOSUM62+F297 8.2
WAG (Whelan and Goldman)+F291 8.1
WAG (Whelan and Goldman)236 6.6
IAV (Influenza A virus)+F218 6.1
HIV (within host)+F217 6.0
IAV (Influenza A virus)207 5.8
BLOSUM62160 4.4
LG (Le and Gascuel)146 4.1

GARD

GARD usage summary as of Thu Sep 21 00:00:40 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days28 28.00 19.82104-281 1249.50555165-11010 469.75 110.5035-5404
Last 7 days85 12.14 17.86104-281 2020.71555165-11979 772.3222435-5404
Last 30 days260 8.67 31.50 17.504-281 1999.6775343-12774 959.4127524-5672
Lifetime (3949 days)72064 18.25 26.65182-300 2028.64111020-46625 1267.903681-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
060375 83.8
HKY855991 8.3
010000860 1.2
REV830 1.2
TRN93558 0.8
F81520 0.7
010232226 0.3
012212218 0.3
010230182 0.3
012232144 0.2
delta AIC rangeTimes found% found
0-1026032 36.1
10-202863 4.0
20-302311 3.2
30-402155 3.0
40-501758 2.4
50-601915 2.7
60-701363 1.9
70-801264 1.8
80-901170 1.6
90-1001045 1.5
> 10030188 41.9
Number of breakpointsTimes found% found
021846 30.3
118261 25.3
211382 15.8
36634 9.2
44040 5.6
52812 3.9
61820 2.5
71379 1.9
8920 1.3
9755 1.0
≥ 102215 3.1

SBP

SBP usage summary as of Thu Sep 21 00:00:49 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days18 18.00 52.28526-281 4.0631-18 471.22 192.500-6079
Last 7 days47 6.71 58.74524-342 3.1111-18 587.871930-6079
Last 30 days139 4.63 48.39154-397 7.7331-81 464.13520-6490
Lifetime (1596 days)19724 12.36 48.46252-656 21.7311-45015 474.70400-279793

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8514050 71.2
REV1311 6.6
010000565 2.9
F81499 2.5
TRN93498 2.5
0123455218 1.1
010232215 1.1
012012137 0.7
0112304567111 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-108549 43.3
10-20878 4.5
20-30740 3.8
30-40598 3.0
40-50483 2.4
50-60385 2.0
60-70338 1.7
70-80352 1.8
80-90275 1.4
90-100287 1.5
> 1006839 34.7

PARRIS

PARRIS usage summary as of Thu Sep 21 00:00:51 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days12 12.00 16.921712-28 1050.581026724-1487 316.17 268.50130-642
Last 7 days24 3.43 16.08176-28 920.54100663-2201 484.92 268.5022-3605
Last 30 days97 3.23 18.74173-68 518.6326932-2994 273.621222-3605
Lifetime (3704 days)13815 3.73 20.27153-75 482.563267-11903 412.811381-35284

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY857737 56.0
F811032 7.5
REV985 7.1
TRN93713 5.2
010000429 3.1
012012250 1.8
001101165 1.2
012212152 1.1
012032123 0.9
010230119 0.9
p-values rangeTimes found% found
0-0.12559 18.5
0.1-0.2485 3.5
0.2-0.3440 3.2
0.3-0.4338 2.4
0.4-0.5320 2.3
0.5-0.6369 2.7
0.6-0.7351 2.5
0.7-0.8339 2.5
0.8-0.9338 2.4
0.9-18276 59.9

GA Branch

GABranch usage summary as of Thu Sep 21 00:00:53 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00121212-12115611561156-1156595159515951-5951
Last 7 days28 4.00 11.64119-18 322.3227646-1156 2859.141442908-31746
Last 30 days70 2.33 12.07113-2769038646-7790 3920.2615593-53677
Lifetime (3697 days)11459 3.10 13.73123-30 513.953299-11628 5316.9015061-636439

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858203 71.6
REV610 5.3
010000568 5.0
F81409 3.6
TRN93280 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
197 0.8
24204 36.7
33880 33.9
42137 18.6
5750 6.5
6224 2.0
7109 1.0
835 0.3
923 0.2

CMS

CMS usage summary as of Thu Sep 21 00:00:54 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00121212-12115611561156-1156260032600326003-26003
Last 7 days5 0.71 26.40269-53 1332.40115635-288615050.4016595829-26206
Last 30 days15 0.50 45.60264-112 794.8749535-288617554.875484829-86342
Lifetime (2788 days)2976 1.07 33.64243-120 533.323327-1079817543.19 3915.5059-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10182 6.1
10-20135 4.5
20-30181 6.1
30-40209 7.0
40-50232 7.8
50-60164 5.5
60-70165 5.5
70-80123 4.1
80-90164 5.5
90-100105 3.5
> 1001316 44.2
Number of rate classesTimes found% found
10 0.0
21901 63.9
3642 21.6
4244 8.2
596 3.2
644 1.5
714 0.5
81 0.0
90 0.0
≥ 1034 1.1

DEPS

DEPS usage summary as of Thu Sep 21 00:00:54 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days13 1.86 66.54856-95 2795.923431410-3439 967.15103224-1979
Last 30 days20 0.67 56.25715-95 1996.40 2486.50193-3439 1079.15 528.5010-8428
Lifetime (2667 days)2619 0.98 31.17243-100 577.454479-6985 414.10992-31585

Subtyping

SCUEAL usage summary as of Thu Sep 21 00:00:55 2017 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days54975497.00 79.2440-500
Last 7 days5497785.29 79.2440-500
Last 30 days5497183.23 79.2440-500
Lifetime (3002 days)6801 2.27 85.4950-500

Top 10 Subtypes (out of 581430 sequences)

SubtypesTimes found% found
B223749 38.5
C104851 18.0
G42436 7.3
A136189 6.2
Complex24103 4.1
D16634 2.9
AE15906 2.7
CRF1411515 2.0
F18599 1.5
B,C recombinant7545 1.3

Coevolution

BGM usage summary as of Thu Sep 21 00:00:56 2017 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days2 2.00171712-22 4.53 4.53 3.23- 5.83 766.50 766.50745-788
Last 7 days18 2.57 39.94173-267 1.39 0.75 0.11- 5.83 205.89 12.500-926
Last 30 days71 2.37 59.35241-427 2.201 0.02- 22.67 349.15210-3896
Lifetime (1596 days)8550 5.36 64.77300-1033 2.26 0.97 0.01-263 2620.44 94.500-2900666

UCSD Viral Evolution Group 2004-2017