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SLAC

SLAC usage summary as of Fri Mar 24 00:00:02 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days69 69.00 60.46455-476 486.2332552-3806 24.30 8.05 0.63- 154.58
Last 7 days236 33.71 68.51433-476 474.9334023-3806 18.81 5.87 0.37- 283.43
Last 30 days958 31.93 60.48433-476 526.9232511-5367 13.23 5.49 0.28- 627.88
Lifetime (2315 days)72723 31.41 53.05253-684 484.093251-11903 23.48 6.66 0.16- 7571.98

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8538355 52.7
TRN939778 13.4
REV8259 11.4
F813099 4.3
010232852 1.2
010230821 1.1
012212748 1.0
012012659 0.9
010000632 0.9
012232569 0.8
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 0.6 16.360456 83.1
0.05 0.6 14.59304 12.8
0.2 0.9 17.71059 1.5
0.25 2.5 26.3567 0.8
0.01 0.8 9.8484 0.7
0.5 4.3 53.1439 0.6
0.15 3.0 14.682 0.1
0.0024 0.0 2.345 0.1
0.3 0.2 20.543 0.1
0.0048 0.0 0.533 0.0

FEL

FEL usage summary as of Fri Mar 24 00:00:13 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days47 47.00 81.96508-476 516.79325104-3806 287.551117-3211
Last 7 days169 24.14 65.22314-476 590.8846872-3806 171.77606-3211
Last 30 days720 24.00 66.66383-500 600.0133211-5367 167.17652-4643
Lifetime (1415 days)88434 62.50 43.48233-787 472.433251-10798 139.47430-26278

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8539839 45.0
REV12127 13.7
TRN938474 9.6
F814096 4.6
0100003884 4.4
0102321902 2.2
0120121250 1.4
0122121206 1.4
0102301028 1.2
001101849 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.2 23.971588 81.0
0.05 0.9 18.813280 15.0
0.2 2.2 28.51622 1.8
0.25 3.4 33.1727 0.8
0.01 0.5 14.8451 0.5
0.5 5.5 44.9184 0.2
0.15 3.1 21.3119 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 Fri Mar 24 00:00:26 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days12 12.00 17.42118-50 390.92 401.50104-662170 64.5014-698
Last 7 days73 10.43 29.79244-75 509.5846960-3806 197.29492-2198
Last 30 days200 6.67 29.00243-75 556.8646944-5367 309.67 110.502-4117
Lifetime (1414 days)49643 35.11 20.26152-110 476.943171-10798 359.121060-37794

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8526336 53.1
REV5234 10.5
TRN932804 5.6
F812674 5.4
0100002316 4.7
012012925 1.9
001101657 1.3
010232645 1.3
012212573 1.2
012032462 0.9
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.4 27.044757 90.2
100 4.3 22.61224 2.5
90 19.9 10.4868 1.7
20 7.0 37.1759 1.5
10 5.8 31.5711 1.4
95 2.6 26.0533 1.1
40 2.5 24.5144 0.3
80 3.5 27.390 0.2
30 10.2 20.689 0.2
0.1 51.8 68.562 0.1

TOGGLE

Toggle usage summary as of Fri Mar 24 00:00:32 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29 42.50 42.5011-7451251288-936427427317-537
Last 30 days11 0.37 29.362511-74 679.8233288-1980 2291.091257317-10521
Lifetime (2495 days)825 0.33 48.87387-150 581.7333016-3789 3930.84198131-42841

Model Select.

ModelSelection usage summary as of Fri Mar 24 00:00:34 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days24 24.0080459-476 309.4032590-488
Last 7 days198 28.29 56.75393-476 456.9732565-3806
Last 30 days893 29.77 50.06383-500 509.123259-10490
Lifetime (1415 days)84226 59.52 40.98213-656 507.793251-11935

Top 10 Models

ModelTimes selected% selected
HKY8520466 24.3
TRN9310962 13.0
F817533 8.9
0102323851 4.6
0120122651 3.1
0122122486 3.0
0102301935 2.3
0011011807 2.1
0122321776 2.1
0120321733 2.1

Protein Model Select.

ModelSelectionP usage summary as of Fri Mar 24 00:00:42 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days1 1.00161616-16163163163-163
Last 7 days3 0.43291610-6118716386-312
Last 30 days25 0.83 54.08343-389 1054.5636886-6985
Lifetime (3216 days)3412 1.06 44.13242-498 616.704333-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F501 14.7
JTT (Jones,Taylor,Thornton)378 11.1
WAG (Whelan and Goldman)+F277 8.1
BLOSUM62+F275 8.1
WAG (Whelan and Goldman)231 6.8
HIV (within host)+F208 6.1
IAV (Influenza A virus)207 6.1
IAV (Influenza A virus)+F196 5.7
BLOSUM62145 4.2
LG (Le and Gascuel)140 4.1

GARD

GARD usage summary as of Fri Mar 24 00:00:44 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days13 13.00 12.2365-46 1583.69858156-9506 802.8574188-2623
Last 7 days67 9.57 22.73115-134 1691.181368103-10272 882.1241365-3927
Last 30 days291 9.70 41.57233-297 1756.6199653-11566 1399.2059359-13803
Lifetime (3768 days)70266 18.65 26.45182-300 2029.24111320-46625 1253.413631-174213

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
058577 83.4
HKY855991 8.5
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
0-1025121 35.8
10-202780 4.0
20-302252 3.2
30-402086 3.0
40-501688 2.4
50-601893 2.7
60-701337 1.9
70-801253 1.8
80-901157 1.6
90-1001023 1.5
> 10029676 42.2
Number of breakpointsTimes found% found
021034 29.9
117796 25.3
211099 15.8
36519 9.3
43980 5.7
52795 4.0
61803 2.6
71360 1.9
8912 1.3
9753 1.1
≥ 102215 3.2

SBP

SBP usage summary as of Fri Mar 24 00:00:53 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days45 6.43 28.76163-470 2.0411-13 158.56253-3539
Last 30 days132 4.40 60.46 28.503-470 7.7911-186 596.89 48.500-14704
Lifetime (1415 days)18888 13.35 47.04252-656 21.7311-45015 453.20400-279793

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8513308 70.5
REV1308 6.9
010000565 3.0
TRN93497 2.6
F81488 2.6
010232214 1.1
0123455195 1.0
012012136 0.7
0112304567108 0.6
010230104 0.6
IC improvement rangeTimes found% found
0-108175 43.3
10-20838 4.4
20-30704 3.7
30-40564 3.0
40-50466 2.5
50-60369 2.0
60-70328 1.7
70-80337 1.8
80-90263 1.4
90-100281 1.5
> 1006563 34.7

PARRIS

PARRIS usage summary as of Fri Mar 24 00:00:57 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days11 11.00887-9 197.8210441-662 46.732717-152
Last 7 days56 8.00 15.07 8.504-61 333.9334931-1288 68.43 56.509-228
Last 30 days96 3.20 16.25123-61 461.51 351.5023-2367 189.51757-3486
Lifetime (3523 days)13297 3.77 20.24153-75 485.093277-11903 417.351371-35284

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY857422 55.8
F81978 7.4
REV965 7.3
TRN93688 5.2
010000429 3.2
012012232 1.7
001101159 1.2
012212145 1.1
010230117 0.9
012032114 0.9
p-values rangeTimes found% found
0-0.12479 18.6
0.1-0.2459 3.5
0.2-0.3425 3.2
0.3-0.4321 2.4
0.4-0.5310 2.3
0.5-0.6359 2.7
0.6-0.7332 2.5
0.7-0.8325 2.4
0.8-0.9321 2.4
0.9-17966 59.9

GA Branch

GABranch usage summary as of Fri Mar 24 00:00:58 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00111111-11341434143414-3414163651636516365-16365
Last 7 days6 0.86 17.17 16.5011-26 1229.1718883-3414 6855.50 3804.50432-16365
Last 30 days37 1.23 13.59123-26 1124.7660861-5367 6234.1111424-64481
Lifetime (3516 days)11152 3.17 13.72123-30 512.943299-11628 5340.8415071-636439

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY857904 70.9
REV609 5.5
010000568 5.1
F81407 3.6
TRN93279 2.5
012012130 1.2
001101107 1.0
01221264 0.6
01001263 0.6
00001060 0.5
the number of dN/dS classes rangeTimes found% found
196 0.9
24083 36.6
33780 33.9
42085 18.7
5725 6.5
6222 2.0
7105 0.9
834 0.3
922 0.2

CMS

CMS usage summary as of Fri Mar 24 00:01:00 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00999-9318318318-318271527152715-2715
Last 7 days6 0.86 34.67349-76 2339.17551104-1049056690.17 4034.501872-290261
Last 30 days28 0.93 39.11273-119 983.2542944-1049057022.43 6663.5083-290261
Lifetime (2607 days)2841 1.09 33.27243-120 533.683327-1079816960.36382959-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10178 6.3
10-20127 4.5
20-30175 6.2
30-40203 7.1
40-50223 7.8
50-60157 5.5
60-70162 5.7
70-80109 3.8
80-90159 5.6
90-100100 3.5
> 1001248 43.9
Number of rate classesTimes found% found
10 0.0
21819 64.0
3613 21.6
4230 8.1
592 3.2
640 1.4
712 0.4
81 0.0
90 0.0
≥ 1034 1.2

DEPS

DEPS usage summary as of Fri Mar 24 00:01:00 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days5 0.17 9.8053-25165533187-6985 36.403910-66
Lifetime (2486 days)2521 1.01 31.10243-100 555.644479-6985 408.47962-31585

Subtyping

SCUEAL usage summary as of Fri Mar 24 00:01:01 2017 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days49824982.00 76.4740-500
Last 7 days4982711.71 76.4740-500
Last 30 days4982166.07 76.4740-500
Lifetime (2821 days)6286 2.23 83.8150-500

Top 10 Subtypes (out of 526823 sequences)

SubtypesTimes found% found
B206777 39.2
C96207 18.3
G40371 7.7
A132909 6.2
Complex21426 4.1
D15882 3.0
AE14667 2.8
CRF1411301 2.1
F18037 1.5
B,C recombinant6107 1.2

Coevolution

BGM usage summary as of Fri Mar 24 00:01:03 2017 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days32 1.07 79.84223-775 2.53 0.96 0.02- 45.67 434.25720-6853
Lifetime (1415 days)8239 5.82 64.69300-1033 2.26 0.97 0.01-263 2693.86970-2900666

UCSD Viral Evolution Group 2004-2017