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SLAC

SLAC usage summary as of Tue Oct 22 00:00:01 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3257 days)92479 28.39 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 Tue Oct 22 00:00:34 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days4 4.00 92.508560-140 233.7517875-504 110.758317-260
Last 7 days23 3.29 49.83483-140 462.5244975-2123 167.749616-609
Last 30 days123 4.10 46.76323-499 600.2432532-3958 448.59672-18955
Lifetime (2357 days)102269 43.39 44.31243-787 484.083251-11276 155.04450-51470

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8546251 45.2
REV13220 12.9
TRN9310052 9.8
F815261 5.1
0100003926 3.8
0102322082 2.0
0120121581 1.5
0122121386 1.4
0102301244 1.2
012032996 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.182693 80.9
0.05 0.9 19.115136 14.8
0.2 2.1 29.82118 2.1
0.25 3.1 32.5909 0.9
0.01 0.4 14.7520 0.5
0.5 5.9 43.2214 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 Tue Oct 22 00:00:57 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days12 1.71 18.67179-30 500.58303238-2123 803.2510415-5867
Last 30 days94 3.13 28.95313-69 748.56 480.50113-3957 1060.951980-39638
Lifetime (2356 days)56983 24.19 20.68162-110 485.463231-10798 389.141110-54132

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8530213 53.0
REV5666 9.9
F813374 5.9
TRN933336 5.9
0100002339 4.1
0120121202 2.1
001101728 1.3
012212704 1.2
010232694 1.2
012032614 1.1
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.951546 90.5
100 4.3 22.41301 2.3
90 19.2 11.2900 1.6
20 7.2 35.9820 1.4
10 5.8 31.9747 1.3
95 2.2 30.8714 1.3
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 Tue Oct 22 00:01:04 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days1 0.03575757-57293293293-293102781027810278-10278
Lifetime (3437 days)1079 0.31 47.63377-150 571.2335016-3789 3787.24197331-42841

Model Select.

ModelSelection usage summary as of Tue Oct 22 00:01:06 2019 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days5 5.009910460-140 257.4022675-504
Last 7 days20 2.86 78.05 73.5013-140 409.70 314.5075-2123
Last 30 days196 6.53 39.42253-289 751.2780732-3958
Lifetime (2357 days)100725 42.73 43.68223-656 520.033251-11935

Top 10 Models

ModelTimes selected% selected
HKY8524153 24.0
TRN9312979 12.9
F818672 8.6
0102324314 4.3
0120123526 3.5
0122123043 3.0
0102302447 2.4
0120322399 2.4
0122322398 2.4
0011012096 2.1

Protein Model Select.

ModelSelectionP usage summary as of Tue Oct 22 00:01:15 2019 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days2 0.07 53.50 53.5011-9619271927318-3536
Lifetime (4158 days)3879 0.93 46.47252-500 652.084443-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F562 14.5
JTT (Jones,Taylor,Thornton)406 10.5
BLOSUM62+F326 8.4
WAG (Whelan and Goldman)+F321 8.3
HIV (within host)+F253 6.5
WAG (Whelan and Goldman)244 6.3
IAV (Influenza A virus)+F241 6.2
IAV (Influenza A virus)225 5.8
BLOSUM62168 4.3
LG (Le and Gascuel)162 4.2

GARD

GARD usage summary as of Tue Oct 22 00:01:17 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days3 3.00 103.3310466-140860678390-1512 744.33640227-1366
Last 7 days15 2.14 61.605711-143 1432.27909279-6369 1313.13736227-4357
Last 30 days99 3.30 24.30163-143 2377.602529171-11871 2229.591147147-72780
Lifetime (4710 days)75236 15.97 26.86182-300 2036.16111620-46625 1288.543831-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
063547 84.5
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
0-1027312 36.3
10-202998 4.0
20-302425 3.2
30-402258 3.0
40-501853 2.5
50-601956 2.6
60-701432 1.9
70-801316 1.7
80-901219 1.6
90-1001082 1.4
> 10031385 41.7
Number of breakpointsTimes found% found
022974 30.5
119032 25.3
211937 15.9
36944 9.2
44237 5.6
52909 3.9
61879 2.5
71413 1.9
8935 1.2
9761 1.0
≥ 102215 2.9

SBP

SBP usage summary as of Tue Oct 22 00:01:26 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days9 1.29 23.44243-53 1.6711-3 656.112348-1983
Last 30 days18 0.60 67.17 39.503-274 2.2211-11 3229.392638-36189
Lifetime (2357 days)20785 8.82 49.86252-656 21.8011-45015 598.05420-683633

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8515031 72.3
REV1315 6.3
010000565 2.7
F81503 2.4
TRN93502 2.4
0123455244 1.2
010232215 1.0
012012137 0.7
0112304567119 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-109012 43.4
10-20899 4.3
20-30788 3.8
30-40644 3.1
40-50510 2.5
50-60409 2.0
60-70358 1.7
70-80376 1.8
80-90283 1.4
90-100317 1.5
> 1007189 34.6

PARRIS

PARRIS usage summary as of Tue Oct 22 00:01:30 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14303030-30238238238-238797979-79
Last 30 days6 0.20 23.67 23.509-38 882.50285227-3957 666.50 122.5030-3448
Lifetime (4465 days)14428 3.23 20.12153-75 486.003297-11903 426.761371-48648

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858168 56.6
F811068 7.4
REV1008 7.0
TRN93758 5.3
010000429 3.0
012012259 1.8
001101166 1.2
012212155 1.1
012032129 0.9
010230125 0.9
p-values rangeTimes found% found
0-0.12627 18.2
0.1-0.2513 3.6
0.2-0.3465 3.2
0.3-0.4365 2.5
0.4-0.5331 2.3
0.5-0.6391 2.7
0.6-0.7370 2.6
0.7-0.8358 2.5
0.8-0.9354 2.5
0.9-18654 60.0

GA Branch

GABranch usage summary as of Tue Oct 22 00:01:32 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days2 0.07303030-30395839583958-3958400934.50400934.50366199-435670
Lifetime (4458 days)11729 2.63 13.73123-30 519.953329-11628 5663.0915211-889396

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858456 72.1
REV614 5.2
010000568 4.8
F81415 3.5
TRN93285 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
24285 36.5
33958 33.7
42199 18.7
5774 6.6
6234 2.0
7117 1.0
838 0.3
925 0.2

CMS

CMS usage summary as of Tue Oct 22 00:01:34 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days4 0.57 37.50 41.5014-53 707.25888158-895399020.5034317211952-897786
Last 30 days6 0.20 44.67 42.5014-86 794.67888158-1364277330.504869211952-897786
Lifetime (3549 days)3205 0.90 33.71243-120 563.813407-1127621213.84406759-3262277

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10184 5.7
10-20147 4.6
20-30189 5.9
30-40217 6.8
40-50243 7.6
50-60178 5.6
60-70174 5.4
70-80128 4.0
80-90175 5.5
90-100108 3.4
> 1001462 45.6
Number of rate classesTimes found% found
10 0.0
22015 62.9
3707 22.1
4272 8.5
5111 3.5
648 1.5
715 0.5
82 0.1
91 0.0
≥ 1034 1.1

DEPS

DEPS usage summary as of Tue Oct 22 00:01:35 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days2 0.07646432-96238823881240-3536531531393-669
Lifetime (3428 days)3406 0.99 35.23303-100 653.205019-11100 500.87 139.502-31585

Subtyping

SCUEAL usage summary as of Tue Oct 22 00:01:37 2019 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days63976397.00 81.9140-500
Last 7 days6397913.86 81.9140-500
Last 30 days6397213.23 81.9140-500
Lifetime (3763 days)7701 2.05 86.9850-500

Top 10 Subtypes (out of 669802 sequences)

SubtypesTimes found% found
B261048 39.0
C116502 17.4
G46059 6.9
A142000 6.3
Complex28191 4.2
AE19805 3.0
D18956 2.8
CRF1411763 1.8
F110612 1.6
B,C recombinant9163 1.4

Coevolution

BGM usage summary as of Tue Oct 22 00:01:39 2019 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (2357 days)8881 3.77 65.10300-1033 2.25 0.98 0.01-263 2866.47920-2900666

UCSD Viral Evolution Group 2004-2019