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SLAC

SLAC usage summary as of Sun Apr 23 00:00:03 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days43 43.00 52.40263-470 273.3023234-711 8.13 2.61 0.34- 85.43
Last 7 days362 51.71 59.39453-499 413.6532534-4249 18.34 8.16 0.34- 294.33
Last 30 days1308 43.60 47.94313-499 458.9432520-4249 17.47 4.96 0.29- 2944.51
Lifetime (2345 days)74031 31.57 52.96253-684 483.653251-11903 23.37 6.63 0.16- 7571.98

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8539108 52.8
TRN939990 13.5
REV8389 11.3
F813146 4.2
010232867 1.2
010230844 1.1
012212754 1.0
012012666 0.9
010000632 0.9
012232575 0.8
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 0.6 16.461595 83.2
0.05 0.6 14.69423 12.7
0.2 0.9 17.81068 1.4
0.25 2.5 26.0579 0.8
0.01 0.8 9.8487 0.7
0.5 4.4 53.7462 0.6
0.15 3.0 14.784 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 Sun Apr 23 00:00:14 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days23 23.00 105.22334-470 239.7411072-564 403.355716-3002
Last 7 days163 23.29 69.15454-470 421.7132545-3392 491.6413311-15594
Last 30 days875 29.17 52.41323-473 491.1332543-4103 231.15734-15594
Lifetime (1445 days)89309 61.81 43.56243-787 472.623251-10798 140.37430-26278

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8540268 45.1
REV12196 13.7
TRN938578 9.6
F814199 4.7
0100003885 4.4
0102321926 2.2
0120121254 1.4
0122121216 1.4
0102301056 1.2
001101850 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.2 24.072349 81.0
0.05 0.9 18.813356 15.0
0.2 2.2 28.71645 1.8
0.25 3.4 33.1737 0.8
0.01 0.5 14.7452 0.5
0.5 5.6 44.5186 0.2
0.15 3.0 21.4121 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 23 00:00:28 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days6 6.00 25.17 14.508-70 246.6716372-611 361.50 238.506-1077
Last 7 days82 11.71 34.28324-70 416.7134972-1660 777.225636-8015
Last 30 days388 12.93 25.97213-70 441.6436155-3423 373.02 175.506-8015
Lifetime (1444 days)50031 34.65 20.30152-110 476.673181-10798 359.231070-37794

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8526616 53.2
REV5251 10.5
TRN932821 5.6
F812694 5.4
0100002316 4.6
012012929 1.9
001101657 1.3
010232654 1.3
012212575 1.1
012032462 0.9
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.4 27.145134 90.2
100 4.3 22.51228 2.5
90 19.9 10.4868 1.7
20 7.0 37.0762 1.5
10 5.8 31.4712 1.4
95 2.6 26.0533 1.1
40 2.5 24.5144 0.3
80 3.5 27.791 0.2
30 10.2 20.689 0.2
0.1 51.0 69.063 0.1

TOGGLE

Toggle usage summary as of Sun Apr 23 00:00:34 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days11 0.37 66.181018-119 397.4552162-549 4613.271363188-15351
Lifetime (2525 days)836 0.33 49.09 38.507-150 579.31 331.5016-3789 3939.82 1977.5031-42841

Model Select.

ModelSelection usage summary as of Sun Apr 23 00:00:36 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days17 17.00 27.18304-45 252.1231172-427
Last 7 days220 31.43 46.34333-390 477.8032545-3422
Last 30 days870 29.00 48.98 29.503-489 499.703259-11830
Lifetime (1445 days)85096 58.89 41.06213-656 507.713251-11935

Top 10 Models

ModelTimes selected% selected
HKY8520654 24.3
TRN9311116 13.1
F817593 8.9
0102323892 4.6
0120122698 3.2
0122122504 2.9
0102301980 2.3
0011011820 2.1
0122321789 2.1
0120321750 2.1

Protein Model Select.

ModelSelectionP usage summary as of Sun Apr 23 00:00:44 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days2 2.0010103-17 773.50 773.50272-1275
Last 7 days20 2.86 33.8573-494 818.25 552.5083-4563
Last 30 days37 1.23 81.38143-499 687.7048683-4563
Lifetime (3246 days)3449 1.06 44.53242-499 617.464343-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F507 14.7
JTT (Jones,Taylor,Thornton)384 11.1
BLOSUM62+F282 8.2
WAG (Whelan and Goldman)+F280 8.1
WAG (Whelan and Goldman)232 6.7
HIV (within host)+F208 6.0
IAV (Influenza A virus)207 6.0
IAV (Influenza A virus)+F197 5.7
BLOSUM62146 4.2
LG (Le and Gascuel)142 4.1

GARD

GARD usage summary as of Sun Apr 23 00:00:46 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days11 11.00 77.457018-297 6754.0910161330-10161 3256.553828599-4526
Last 7 days71 10.14 60.21344-297 5163.20232472-10988 3692.993751250-46645
Last 30 days376 12.53 33.53163-297 2631.76136772-12309 1917.78 921.5038-46645
Lifetime (3798 days)70642 18.60 26.48182-300 2032.44111320-46625 1256.953651-174213

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
058953 83.5
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
0-1025260 35.8
10-202793 4.0
20-302259 3.2
30-402106 3.0
40-501714 2.4
50-601899 2.7
60-701346 1.9
70-801256 1.8
80-901159 1.6
90-1001031 1.5
> 10029819 42.2
Number of breakpointsTimes found% found
021166 30.0
117911 25.4
211164 15.8
36554 9.3
43996 5.7
52797 4.0
61806 2.6
71366 1.9
8914 1.3
9753 1.1
≥ 102215 3.1

SBP

SBP usage summary as of Sun Apr 23 00:00:56 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days24 24.00 46.621616-470 1.2911-5 961.46 101.5022-15932
Last 7 days48 6.86 47.23163-470 4.9411-77 1010.79 160.503-15932
Last 30 days156 5.20 49.63173-497 8.0311-135 753.99 57.500-15932
Lifetime (1445 days)19044 13.18 47.07242-656 21.6211-45015 455.67400-279793

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8513439 70.6
REV1310 6.9
010000565 3.0
TRN93497 2.6
F81489 2.6
010232214 1.1
0123455206 1.1
012012136 0.7
0112304567108 0.6
010230104 0.5
IC improvement rangeTimes found% found
0-108226 43.2
10-20844 4.4
20-30709 3.7
30-40576 3.0
40-50471 2.5
50-60372 2.0
60-70329 1.7
70-80339 1.8
80-90265 1.4
90-100282 1.5
> 1006631 34.8

PARRIS

PARRIS usage summary as of Sun Apr 23 00:00:59 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00181818-18193193193-193189518951895-1895
Last 7 days6 0.86 23.502313-32 153.6716483-199 482.8323671-1895
Last 30 days76 2.53 18.49144-63 533.0436838-4103 241.7112410-1895
Lifetime (3553 days)13373 3.76 20.23153-75 485.373277-11903 416.361371-35284

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY857474 55.9
F81982 7.3
REV972 7.3
TRN93691 5.2
010000429 3.2
012012232 1.7
001101159 1.2
012212147 1.1
010230117 0.9
012032114 0.9
p-values rangeTimes found% found
0-0.12492 18.6
0.1-0.2464 3.5
0.2-0.3428 3.2
0.3-0.4325 2.4
0.4-0.5313 2.3
0.5-0.6360 2.7
0.6-0.7332 2.5
0.7-0.8326 2.4
0.8-0.9322 2.4
0.9-18011 59.9

GA Branch

GABranch usage summary as of Sun Apr 23 00:01:00 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00303030-30232232232-232777077707770-7770
Last 7 days11 1.57 13.9196-30 616.2726383-2244 2998.452153889-7770
Last 30 days39 1.30 16.44155-30 550.0547473-2244 5508.77368082-23303
Lifetime (3546 days)11191 3.16 13.73123-30 513.073299-11628 5341.4315111-636439

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY857942 71.0
REV609 5.4
010000568 5.1
F81408 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
24089 36.5
33796 33.9
42096 18.7
5731 6.5
6222 2.0
7105 0.9
834 0.3
922 0.2

CMS

CMS usage summary as of Sun Apr 23 00:01:02 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29707047-93 199.50 199.50167-23226870.5026870.508980-44761
Last 30 days18 0.60 50.61416-101 689.89420113-379998202.06 7595.503001-680451
Lifetime (2637 days)2859 1.08 33.38243-120 534.673337-1079817471.85387259-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10178 6.2
10-20127 4.4
20-30175 6.1
30-40205 7.2
40-50224 7.8
50-60157 5.5
60-70162 5.7
70-80109 3.8
80-90160 5.6
90-100100 3.5
> 1001262 44.1
Number of rate classesTimes found% found
10 0.0
21827 63.9
3617 21.6
4232 8.1
592 3.2
643 1.5
713 0.5
81 0.0
90 0.0
≥ 1034 1.2

DEPS

DEPS usage summary as of Sun Apr 23 00:01:02 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00212121-21506506506-506228228228-228
Last 7 days13 1.86 11.54113-25 1182.3867383-4563 193.7717225-406
Last 30 days20 0.67 16.45113-59 929.25 581.5083-4563 457.501545-5128
Lifetime (2516 days)2541 1.01 30.98243-100 558.584479-6985 408.86972-31585

Subtyping

SCUEAL usage summary as of Sun Apr 23 00:01:03 2017 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days50415041.00 76.2040-500
Last 7 days5041720.14 76.2040-500
Last 30 days5041168.03 76.2040-500
Lifetime (2851 days)6345 2.23 83.5350-500

Top 10 Subtypes (out of 529980 sequences)

SubtypesTimes found% found
B208392 39.3
C96372 18.2
G40432 7.6
A133142 6.3
Complex21635 4.1
D16027 3.0
AE14822 2.8
CRF1411301 2.1
F18086 1.5
B,C recombinant6123 1.2

Coevolution

BGM usage summary as of Sun Apr 23 00:01:05 2017 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00393939-39 1.36 1.36 1.36- 1.36328328328-328
Last 7 days19 2.71 41.42342-289 1.10 0.74 0.16-6 134.2150-862
Last 30 days81 2.70 87.74292-995 1.24 0.88 0.08-6 975.31160-17738
Lifetime (1445 days)8320 5.76 64.91300-1033 2.25 0.97 0.01-263 2677.13960-2900666

UCSD Viral Evolution Group 2004-2017