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SLAC

SLAC usage summary as of Mon Nov 20 00:00:03 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days7 7.00 72.71218-385 759.71652130-1173 15.41 3.06 0.73- 93.69
Last 7 days188 26.86 49.92453-400 633.1032571-4818 12.61 8.07 0.56- 251.34
Last 30 days714 23.80 49.46373-461 656.96 378.5023-5319 14.52 6.62 0.24- 1202.30
Lifetime (2556 days)83225 32.56 52.00253-684 483.113251-11903 21.94 6.30 0.16- 7571.98

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8543417 52.2
TRN9312381 14.9
REV9025 10.8
F813657 4.4
010232933 1.1
010230923 1.1
012212813 1.0
012012735 0.9
010000649 0.8
012232646 0.8
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 0.6 16.069766 83.8
0.05 0.6 14.510148 12.2
0.2 0.9 17.01189 1.4
0.25 2.3 25.2666 0.8
0.5 4.4 54.9517 0.6
0.01 0.8 9.5510 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 Mon Nov 20 00:00:15 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days9 9.00 57.11108-385 683.6765297-1173 110.56296-781
Last 7 days270 38.57 44.93 25.503-385 731.5743852-4818 202.42816-3395
Last 30 days758 25.27 47.30253-461 674.6439640-5319 217.52732-11651
Lifetime (1656 days)94881 57.30 44.02243-787 474.223251-11276 141.23440-26278

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8542895 45.2
REV12676 13.4
TRN939242 9.7
F814657 4.9
0100003903 4.1
0102321997 2.1
0120121323 1.4
0122121264 1.3
0102301152 1.2
001101897 0.9
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.176769 80.9
0.05 0.9 19.214259 15.0
0.2 2.1 28.61783 1.9
0.25 3.3 32.7803 0.8
0.01 0.4 14.3483 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 Mon Nov 20 00:00:30 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days5 5.00 20.60168-35 860.201173130-117397377-234
Last 7 days95 13.57 20.17133-74 860.1260752-4818 251.03595-2104
Last 30 days292 9.73 22.53163-75 774.9141352-5319 464.861041-18527
Lifetime (1655 days)52910 31.97 20.45152-110 477.373161-10798 358.691080-38013

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8528142 53.2
REV5469 10.3
TRN933010 5.7
F813001 5.7
0100002325 4.4
012012986 1.9
001101690 1.3
010232671 1.3
012212626 1.2
012032502 0.9
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.447712 90.2
100 4.2 22.51273 2.4
90 19.5 11.0887 1.7
20 7.3 36.2782 1.5
10 5.8 31.7719 1.4
95 2.4 27.8616 1.2
40 2.5 24.5144 0.3
80 3.2 27.199 0.2
30 10.2 20.689 0.2
25 2.5 38.279 0.1

TOGGLE

Toggle usage summary as of Mon Nov 20 00:00:36 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days5 0.17 52.804718-77450409256-829 4555.403090750-11366
Lifetime (2736 days)979 0.36 48.75397-150 568.3834316-3789 3952.91207931-42841

Model Select.

ModelSelection usage summary as of Mon Nov 20 00:00:38 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days11 11.00 54.91168-385 692.9165272-1173
Last 7 days393 56.14 37.55353-385 697.79512 48.33-4818
Last 30 days1063 35.43 43.62243-466 591.694465-4818
Lifetime (1656 days)91008 54.96 41.30223-656 511.923251-11935

Top 10 Models

ModelTimes selected% selected
HKY8521867 24.0
TRN9312027 13.2
F818157 9.0
0102324087 4.5
0120122914 3.2
0122122658 2.9
0102302154 2.4
0120321968 2.2
0122321959 2.2
0011011916 2.1

Protein Model Select.

ModelSelectionP usage summary as of Mon Nov 20 00:00:48 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days13 1.86 29.462911-49 439.23352104-1912
Last 30 days36 1.20 48.97404-202 622.03 342.50104-3907
Lifetime (3457 days)3667 1.06 45.56252-499 643.844403-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F541 14.8
JTT (Jones,Taylor,Thornton)396 10.8
BLOSUM62+F305 8.3
WAG (Whelan and Goldman)+F300 8.2
WAG (Whelan and Goldman)238 6.5
IAV (Influenza A virus)+F227 6.2
HIV (within host)+F222 6.1
IAV (Influenza A virus)208 5.7
BLOSUM62163 4.4
LG (Le and Gascuel)147 4.0

GARD

GARD usage summary as of Mon Nov 20 00:00:50 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days5 5.00 7.6084-9 2202.602208390-3414 1012.4081765-2708
Last 7 days96 13.71 36.92353-170 2671.17 2243.50246-14454 2109.38 2128.5040-4492
Last 30 days352 11.73 37.31213-299 2136.141347145-15957 1414.11 573.5017-20657
Lifetime (4009 days)72633 18.12 26.72182-300 2029.88111020-46625 1269.423691-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
060944 83.9
HKY855991 8.2
010000860 1.2
REV830 1.1
TRN93558 0.8
F81520 0.7
010232226 0.3
012212218 0.3
010230182 0.3
012232144 0.2
delta AIC rangeTimes found% found
0-1026294 36.2
10-202889 4.0
20-302324 3.2
30-402177 3.0
40-501769 2.4
50-601921 2.6
60-701374 1.9
70-801278 1.8
80-901183 1.6
90-1001050 1.4
> 10030374 41.8
Number of breakpointsTimes found% found
022079 30.4
118404 25.3
211490 15.8
36673 9.2
44063 5.6
52823 3.9
61825 2.5
71386 1.9
8920 1.3
9755 1.0
≥ 102215 3.0

SBP

SBP usage summary as of Mon Nov 20 00:01:00 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days10 1.43 44.801911-162311-6 756.40 65.504-3687
Last 30 days101 3.37 37.15193-325 12.4211-310 366.85570-3687
Lifetime (1656 days)19936 12.04 48.50242-656 21.6011-45015 474.91410-279793

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8514250 71.5
REV1311 6.6
010000565 2.8
F81500 2.5
TRN93499 2.5
0123455221 1.1
010232215 1.1
012012137 0.7
0112304567112 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-108618 43.2
10-20883 4.4
20-30743 3.7
30-40606 3.0
40-50497 2.5
50-60390 2.0
60-70348 1.7
70-80363 1.8
80-90277 1.4
90-100291 1.5
> 1006920 34.7

PARRIS

PARRIS usage summary as of Mon Nov 20 00:01:04 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00999-9130130130-130999-9
Last 7 days19 2.71 19.21134-46 1032.89772130-2316 450.42919-1932
Last 30 days58 1.93 23.91194-75 751.5054771-3423 477.641693-4392
Lifetime (3764 days)13919 3.70 20.27153-75 483.863277-11903 413.071381-35284

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY857797 56.0
F811045 7.5
REV992 7.1
TRN93719 5.2
010000429 3.1
012012250 1.8
001101166 1.2
012212152 1.1
012032127 0.9
010230119 0.9
p-values rangeTimes found% found
0-0.12573 18.5
0.1-0.2491 3.5
0.2-0.3442 3.2
0.3-0.4341 2.4
0.4-0.5321 2.3
0.5-0.6369 2.7
0.6-0.7354 2.5
0.7-0.8345 2.5
0.8-0.9341 2.4
0.9-18342 59.9

GA Branch

GABranch usage summary as of Mon Nov 20 00:01:07 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days4 4.00121010-18 203.2510497-508 1435.50511492-4228
Last 7 days5 0.71 12.801010-18 245.6010497-508 1582.80519492-4228
Last 30 days35 1.17 14.43165-27 654.7741597-3632 4624.3421592-23398
Lifetime (3757 days)11522 3.07 13.72123-30 513.823299-11628 5309.87 1505.501-636439

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858261 71.7
REV611 5.3
010000568 4.9
F81412 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
199 0.9
24227 36.7
33898 33.8
42149 18.7
5754 6.5
6226 2.0
7111 1.0
835 0.3
923 0.2

CMS

CMS usage summary as of Mon Nov 20 00:01:09 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days3 0.43 12.3333-31 1213.33380380-2880 2508.67278218-7030
Last 30 days22 0.73 34.27323-90 1168.55 406.5058-1127673817.32 3591.50218-916098
Lifetime (2848 days)3018 1.06 33.67243-120 538.263327-1127617980.29395159-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10182 6.0
10-20138 4.6
20-30183 6.1
30-40210 7.0
40-50233 7.7
50-60166 5.5
60-70168 5.6
70-80124 4.1
80-90164 5.4
90-100107 3.5
> 1001343 44.5
Number of rate classesTimes found% found
10 0.0
21923 63.7
3655 21.7
4247 8.2
599 3.3
644 1.5
714 0.5
82 0.1
90 0.0
≥ 1034 1.1

DEPS

DEPS usage summary as of Mon Nov 20 00:01:10 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days4 0.57303015-45 300.50 300.50186-415 148.7514829-270
Last 30 days20 0.67 51.95454-100 698.20333186-2867 620.652645-1977
Lifetime (2727 days)2684 0.98 31.85243-100 581.174399-11100 437.81 99.502-31585

Subtyping

SCUEAL usage summary as of Mon Nov 20 00:01:11 2017 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days55835583.00 79.8040-500
Last 7 days5583797.57 79.8040-500
Last 30 days5583186.10 79.8040-500
Lifetime (3062 days)6887 2.25 85.8750-500

Top 10 Subtypes (out of 591355 sequences)

SubtypesTimes found% found
B227081 38.4
C105130 17.8
G42750 7.2
A138637 6.5
Complex24693 4.2
D16671 2.8
AE16570 2.8
CRF1411520 1.9
F18816 1.5
B,C recombinant7595 1.3

Coevolution

BGM usage summary as of Mon Nov 20 00:01:14 2017 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days22 0.73 26.41112-162 3.46 1.50 0.07- 9.73 507.45 67.500-3443
Lifetime (1656 days)8603 5.20 64.63300-1033 2.26 0.97 0.01-263 2606.43920-2900666

UCSD Viral Evolution Group 2004-2017