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SLAC

SLAC usage summary as of Mon Jun 26 00:00:02 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days14 14.00 33.14 30.505-64 428.2132579-1133 4.02 2.39 0.68- 9.60
Last 7 days303 43.29 54.43273-464 433.0332535-3596 10.15 3.47 0.26- 420.16
Last 30 days1171 39.03 51.83283-500 525.3432523-4887 13.59 3.75 0.26- 420.16
Lifetime (2409 days)77004 31.97 52.62253-684 483.253251-11903 22.94 6.49 0.16- 7571.98

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8540707 52.9
TRN9310634 13.8
REV8569 11.1
F813303 4.3
010232885 1.1
010230867 1.1
012212777 1.0
012012696 0.9
010000635 0.8
012232601 0.8
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 0.6 16.364230 83.4
0.05 0.6 14.59671 12.6
0.2 0.9 17.51099 1.4
0.25 2.4 25.6598 0.8
0.01 0.8 9.7493 0.6
0.5 4.4 54.4492 0.6
0.15 2.9 14.886 0.1
0.0024 0.0 2.345 0.1
0.3 0.2 20.444 0.1
0.0048 0.0 0.533 0.0

FEL

FEL usage summary as of Mon Jun 26 00:00:13 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days131 18.71 76.08223-416 325.5227335-2336 137.35554-1274
Last 30 days722 24.07 51.13283-500 408.5727322-3423 96.62 38.502-2349
Lifetime (1509 days)91054 60.34 43.62243-787 471.643251-10798 140.44430-26278

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8541149 45.2
REV12334 13.5
TRN938814 9.7
F814357 4.8
0100003888 4.3
0102321934 2.1
0120121281 1.4
0122121227 1.3
0102301079 1.2
001101859 0.9
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.2 24.073713 81.0
0.05 0.9 18.613672 15.0
0.2 2.2 28.81678 1.8
0.25 3.3 32.8762 0.8
0.01 0.5 14.7453 0.5
0.5 5.6 44.5186 0.2
0.15 3.0 21.6126 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 Jun 26 00:00:26 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days85 12.14 25.35203-66 529.9525735-2336 746.642293-14431
Last 30 days535 17.83 27.63253-74 376.2524230-3411 472.781441-38013
Lifetime (1508 days)51111 33.89 20.41152-110 475.443161-10798 359.821080-38013

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8527222 53.3
REV5327 10.4
TRN932905 5.7
F812823 5.5
0100002316 4.5
012012951 1.9
001101662 1.3
010232657 1.3
012212584 1.1
012032472 0.9
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.4 27.246058 90.1
100 4.2 22.51255 2.5
90 19.6 10.8880 1.7
20 7.0 36.8766 1.5
10 5.8 31.6716 1.4
95 2.3 27.9607 1.2
40 2.5 24.5144 0.3
80 3.4 27.194 0.2
30 10.2 20.689 0.2
25 2.6 35.575 0.1

TOGGLE

Toggle usage summary as of Mon Jun 26 00:00:32 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days13 0.43 37.384118-74 250.6921192-820 3917.382834986-13631
Lifetime (2589 days)860 0.33 48.87 38.507-150 569.4233016-3789 3951.63198531-42841

Model Select.

ModelSelection usage summary as of Mon Jun 26 00:00:33 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days128 18.29 63.11313-464 532.4232435-3596
Last 30 days703 23.43 52.63283-464 567.2032622-3659
Lifetime (1509 days)86859 57.56 41.13223-656 508.053251-11935

Top 10 Models

ModelTimes selected% selected
HKY8521014 24.2
TRN9311419 13.1
F817794 9.0
0102323932 4.5
0120122763 3.2
0122122556 2.9
0102302037 2.3
0011011842 2.1
0122321835 2.1
0120321791 2.1

Protein Model Select.

ModelSelectionP usage summary as of Mon Jun 26 00:00:41 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days12 1.71 73.42868-120 3209.33 3394.50534-4547
Last 30 days28 0.93 71.46917-1431663 741.5011-4547
Lifetime (3310 days)3519 1.06 44.71242-499 631.384403-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F516 14.7
JTT (Jones,Taylor,Thornton)388 11.0
BLOSUM62+F292 8.3
WAG (Whelan and Goldman)+F282 8.0
WAG (Whelan and Goldman)233 6.6
HIV (within host)+F211 6.0
IAV (Influenza A virus)+F211 6.0
IAV (Influenza A virus)207 5.9
BLOSUM62157 4.5
LG (Le and Gascuel)143 4.1

GARD

GARD usage summary as of Mon Jun 26 00:00:43 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days64 9.14 25.44163-178 1519.061071105-8814 1744.73 690.5019-20182
Last 30 days285 9.50 34.53203-284 1878.511074105-14661 1393.9141419-28613
Lifetime (3862 days)71270 18.45 26.56182-300 2030.37111320-46625 1261.863671-174213

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
059581 83.6
HKY855991 8.4
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
0-1025589 35.9
10-202822 4.0
20-302269 3.2
30-402135 3.0
40-501731 2.4
50-601902 2.7
60-701354 1.9
70-801260 1.8
80-901165 1.6
90-1001037 1.5
> 10030006 42.1
Number of breakpointsTimes found% found
021454 30.1
118079 25.4
211257 15.8
36591 9.2
44018 5.6
52802 3.9
61813 2.5
71372 1.9
8915 1.3
9754 1.1
≥ 102215 3.1

SBP

SBP usage summary as of Mon Jun 26 00:00:53 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days27 3.86 76.19516-231 10.3011-1605111750-1695
Last 30 days118 3.93 86.68 50.504-471 61.87 1.501-5596 583.751570-11811
Lifetime (1509 days)19295 12.79 47.61252-656 21.7811-45015 470.54400-279793

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8513666 70.8
REV1310 6.8
010000565 2.9
TRN93497 2.6
F81493 2.6
010232215 1.1
0123455213 1.1
012012137 0.7
0112304567110 0.6
010230104 0.5
IC improvement rangeTimes found% found
0-108372 43.4
10-20848 4.4
20-30713 3.7
30-40586 3.0
40-50478 2.5
50-60376 1.9
60-70331 1.7
70-80349 1.8
80-90265 1.4
90-100284 1.5
> 1006693 34.7

PARRIS

PARRIS usage summary as of Mon Jun 26 00:00:56 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days9 1.29 24.22215-47 269.6719587-521 169.6712629-386
Last 30 days90 3.00 27.39225-74 289.8025161-1186 314.5314213-3849
Lifetime (3617 days)13587 3.76 20.26153-75 483.233277-11903 415.671381-35284

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY857597 55.9
F811014 7.5
REV975 7.2
TRN93708 5.2
010000429 3.2
012012238 1.8
001101164 1.2
012212147 1.1
010230118 0.9
012032117 0.9
p-values rangeTimes found% found
0-0.12521 18.6
0.1-0.2480 3.5
0.2-0.3432 3.2
0.3-0.4332 2.4
0.4-0.5315 2.3
0.5-0.6365 2.7
0.6-0.7338 2.5
0.7-0.8331 2.4
0.8-0.9327 2.4
0.9-18146 60.0

GA Branch

GABranch usage summary as of Mon Jun 26 00:00:57 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days10 1.43 14.20145-22 308.1039251-521 2484.50124735-8280
Last 30 days50 1.67 14.62143-30 464.8830151-3559 5489.529321-56830
Lifetime (3610 days)11309 3.13 13.73123-30 513.393299-11628 5339.8215071-636439

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858060 71.3
REV609 5.4
010000568 5.0
F81408 3.6
TRN93279 2.5
012012130 1.1
001101107 0.9
01221264 0.6
01001263 0.6
00001060 0.5
the number of dN/dS classes rangeTimes found% found
196 0.8
24136 36.6
33836 33.9
42114 18.7
5738 6.5
6223 2.0
7108 1.0
835 0.3
923 0.2

CMS

CMS usage summary as of Mon Jun 26 00:00:59 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days6 0.86 25.332111-63 323.5040135-424 8485.503238937-36724
Last 30 days25 0.83 40.32247-120 462.5637735-339130244.563356581-622059
Lifetime (2701 days)2911 1.08 33.47243-120 531.303317-1079817610.85389559-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10178 6.1
10-20131 4.5
20-30179 6.1
30-40209 7.2
40-50226 7.8
50-60163 5.6
60-70162 5.6
70-80114 3.9
80-90162 5.6
90-100102 3.5
> 1001285 44.1
Number of rate classesTimes found% found
10 0.0
21859 63.9
3631 21.7
4236 8.1
593 3.2
644 1.5
713 0.4
81 0.0
90 0.0
≥ 1034 1.2

DEPS

DEPS usage summary as of Mon Jun 26 00:00:59 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days8 1.1464 58.508-100 3041.50 3391.50534-3423 1618.12111416-4709
Last 30 days12 0.4053457-100 2160.33 3388.5011-3423 1209.75 399.508-4709
Lifetime (2580 days)2562 0.99 31.03243-100 567.71 449.509-6985 411.65982-31585

Subtyping

SCUEAL usage summary as of Mon Jun 26 00:01:00 2017 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days52365236.00 76.2340-500
Last 7 days5236748.00 76.2340-500
Last 30 days5236174.53 76.2340-500
Lifetime (2915 days)6540 2.24 83.3350-500

Top 10 Subtypes (out of 544967 sequences)

SubtypesTimes found% found
B212035 38.9
C98020 18.0
G41417 7.6
A133960 6.2
Complex22713 4.2
D16174 3.0
AE15178 2.8
CRF1411495 2.1
F18308 1.5
B,C recombinant7350 1.3

Coevolution

BGM usage summary as of Mon Jun 26 00:01:01 2017 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days2 2.00888-8 1.50 1.50 1.50- 1.50555-5
Last 7 days7 1.00 22.86121-95 1.94 1.50 0.23- 6.25 238.7150-985
Last 30 days23 0.77 82.52521-468 1.52 0.71 0.02- 6.78 644.83110-5818
Lifetime (1509 days)8375 5.55 65.00300-1033 2.25 0.97 0.01-263 2666.91960-2900666

UCSD Viral Evolution Group 2004-2017