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SLAC

SLAC usage summary as of Fri Dec 4 00:00:01 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3666 days)92479 25.23 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 Fri Dec 4 00:01:05 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days11 11.00 41.273016-168 3485.6439581353-3958 714.4575326-1006
Last 7 days24 3.43 43.29305-168 2497.04 1996.50251-3958 578.795896-1782
Last 30 days64 2.13 47.47304-275 1549.0585487-9740 303.78985-2062
Lifetime (2766 days)103701 37.49 44.50243-787 487.723251-11276 181.59460-51470

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8547130 45.4
REV13314 12.8
TRN9310140 9.8
F815402 5.2
0100003929 3.8
0102322094 2.0
0120121582 1.5
0122121402 1.4
0102301269 1.2
0120321005 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.083839 80.8
0.05 0.9 19.115342 14.8
0.2 2.1 29.72136 2.1
0.25 3.1 31.9942 0.9
0.01 0.4 14.7523 0.5
0.5 5.9 43.2214 0.2
0.15 2.3 22.7181 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 Fri Dec 4 00:01:46 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days8 8.00 28.253016-30 3632.3839581353-3958 1160.50 1245.5057-1721
Last 7 days21 3.00 25.43305-3822531353251-3958 709.243593-2303
Last 30 days85 2.8325245-62 1115.8576389-9740 291.011103-2303
Lifetime (2765 days)58037 20.99 20.71162-110 488.143231-11542 390.371110-54132

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8530855 53.2
REV5698 9.8
F813525 6.1
TRN933362 5.8
0100002344 4.0
0120121223 2.1
001101730 1.3
012212718 1.2
010232709 1.2
012032619 1.1
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.852462 90.4
100 4.4 22.11318 2.3
90 19.2 11.2901 1.6
20 7.2 35.9824 1.4
95 2.4 31.6764 1.3
10 5.8 31.9747 1.3
40 2.5 24.4145 0.2
25 7.8 34.7115 0.2
80 3.0 28.4110 0.2
30 9.8 20.693 0.2

TOGGLE

Toggle usage summary as of Fri Dec 4 00:01:57 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14232323-23503503503-503159115911591-1591
Last 30 days1 0.03232323-23503503503-503159115911591-1591
Lifetime (3846 days)1091 0.28 47.56377-150 569.2035016-3789 3767.81197331-42841

Model Select.

ModelSelection usage summary as of Fri Dec 4 00:01:59 2020 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days20 20.00 30.65307-55 538.10518133-1008
Last 7 days39 5.57 45.74297-330 550.2850354-2466
Last 30 days126 4.20 35.65234-330 759.2051454-9740
Lifetime (2766 days)102346 37.00 43.81223-656 522.473251-11935

Top 10 Models

ModelTimes selected% selected
HKY8524570 24.0
TRN9313096 12.8
F818884 8.7
0102324379 4.3
0120123587 3.5
0122123087 3.0
0102302483 2.4
0122322434 2.4
0120322430 2.4
0011012114 2.1

Protein Model Select.

ModelSelectionP usage summary as of Fri Dec 4 00:02:14 2020 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days1 0.03151515-15994299429942-9942
Lifetime (4567 days)3945 0.86 46.55252-500 674.714443-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F567 14.4
JTT (Jones,Taylor,Thornton)410 10.4
BLOSUM62+F327 8.3
WAG (Whelan and Goldman)+F325 8.2
HIV (within host)+F272 6.9
WAG (Whelan and Goldman)245 6.2
IAV (Influenza A virus)+F243 6.2
IAV (Influenza A virus)228 5.8
BLOSUM62169 4.3
LG (Le and Gascuel)168 4.3

GARD

GARD usage summary as of Fri Dec 4 00:02:16 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days4 4.00 32.753623-36 1555.501941399-1941 2973.75 3782.50437-3893
Last 7 days18 2.57 30.94237-101 2270.501173399-11874 2158.062437120-3893
Last 30 days69 2.30 27.94215-190 4719.071413360-29220 1384.2387244-3893
Lifetime (5119 days)75874 14.82 26.95182-300 2045.13111620-46625 1292.673871-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
064185 84.6
HKY855991 7.9
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
0-1027558 36.3
10-203019 4.0
20-302443 3.2
30-402272 3.0
40-501868 2.5
50-601974 2.6
60-701449 1.9
70-801325 1.7
80-901225 1.6
90-1001087 1.4
> 10031654 41.7
Number of breakpointsTimes found% found
023199 30.6
119188 25.3
212040 15.9
37012 9.2
44270 5.6
52934 3.9
61898 2.5
71417 1.9
8940 1.2
9761 1.0
≥ 102215 2.9

SBP

SBP usage summary as of Fri Dec 4 00:02:32 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days5 0.71 59.203523-107 12.40171-23 4913.4031144-23026
Last 30 days12 0.40 142.9210421-492 16.33 4.501-73 2825.5887631-23026
Lifetime (2766 days)21192 7.66 50.18252-656 21.7411-45015 602.88440-683633

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8515364 72.5
REV1315 6.2
010000565 2.7
F81503 2.4
TRN93502 2.4
0123455283 1.3
010232215 1.0
012012137 0.6
0112304567122 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-109173 43.3
10-20911 4.3
20-30802 3.8
30-40656 3.1
40-50519 2.4
50-60413 1.9
60-70361 1.7
70-80378 1.8
80-90293 1.4
90-100328 1.5
> 1007358 34.7

PARRIS

PARRIS usage summary as of Fri Dec 4 00:02:37 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00161616-16135313531353-1353199199199-199
Last 7 days6 0.86 13.17105-30 1560.501273251-39581158 107.503-6349
Last 30 days10 0.33 17.70 14.505-34 1070.90863120-3958 723.70 61.503-6349
Lifetime (4874 days)14581 2.99 20.12153-75 489.463297-11903 425.901361-48648

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858250 56.6
F811079 7.4
REV1010 6.9
TRN93771 5.3
010000429 2.9
012012262 1.8
001101166 1.1
012212155 1.1
012032137 0.9
010230125 0.9
p-values rangeTimes found% found
0-0.12665 18.3
0.1-0.2518 3.6
0.2-0.3474 3.3
0.3-0.4371 2.5
0.4-0.5331 2.3
0.5-0.6392 2.7
0.6-0.7373 2.6
0.7-0.8359 2.5
0.8-0.9355 2.4
0.9-18743 60.0

GA Branch

GABranch usage summary as of Fri Dec 4 00:02:40 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days5 5.00 16.801611-30184213531273-395836727.6069331345-166697
Last 7 days7 1.00 13.86115-30 1676.8612731255-395826275.29158018-166697
Last 30 days7 0.23 13.86115-30 1676.8612731255-395826275.29158018-166697
Lifetime (4867 days)11845 2.43 13.74123-30 521.603339-11628 5654.4315151-889396

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858572 72.4
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
24312 36.4
34010 33.9
42226 18.8
5778 6.6
6237 2.0
7118 1.0
839 0.3
926 0.2

CMS

CMS usage summary as of Fri Dec 4 00:02:42 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14353535-35246624662466-2466362336233623-3623
Last 30 days2 0.07 54.50 54.5035-74239923992332-2466 5982.50 5982.503623-8342
Lifetime (3958 days)3279 0.83 33.73243-120 570.223447-1127621081.69404559-3262277

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10192 5.9
10-20151 4.6
20-30193 5.9
30-40222 6.8
40-50246 7.5
50-60180 5.5
60-70177 5.4
70-80129 3.9
80-90178 5.4
90-100111 3.4
> 1001500 45.7
Number of rate classesTimes found% found
10 0.0
22060 62.8
3720 22.0
4279 8.5
5118 3.6
650 1.5
715 0.5
82 0.1
91 0.0
≥ 1034 1.0

DEPS

DEPS usage summary as of Fri Dec 4 00:02:44 2020 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days2 0.07 17.50 17.5015-20 5051.50 5051.50161-9942 36.50 36.5034-39
Lifetime (3837 days)3577 0.93 35.84323-100 733.175289-11100 489.421462-31585

Subtyping

SCUEAL usage summary as of Fri Dec 4 00:02:46 2020 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days70027002.00 91.4240-500
Last 7 days70021000.29 91.4240-500
Last 30 days7002233.40 91.4240-500
Lifetime (4172 days)8306 1.99 94.6350-500

Top 10 Subtypes (out of 785964 sequences)

SubtypesTimes found% found
B310361 39.5
C152262 19.4
G51243 6.5
A146357 5.9
Complex32766 4.2
AE20758 2.6
D19688 2.5
CRF1412892 1.6
F112305 1.6
B,C recombinant9775 1.2

Coevolution

BGM usage summary as of Fri Dec 4 00:02:50 2020 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (2766 days)8881 3.21 65.10300-1033 2.25 0.98 0.01-263 2866.47920-2900666

UCSD Viral Evolution Group 2004-2020