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SLAC

SLAC usage summary as of Sun May 16 00:00:02 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3829 days)92479 24.15 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 Sun May 16 00:00:20 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days16 0.53 39.31 25.506-168 603.88638150-1175 87.94 53.508-353
Lifetime (2929 days)103965 35.50 44.59243-787 488.083251-11276 182.47460-51470

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8547265 45.5
REV13359 12.8
TRN9310156 9.8
F815437 5.2
0100003929 3.8
0102322094 2.0
0120121583 1.5
0122121405 1.4
0102301269 1.2
0120321005 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.084061 80.9
0.05 0.9 19.115377 14.8
0.2 2.1 29.72137 2.1
0.25 3.1 31.9942 0.9
0.01 0.4 14.6524 0.5
0.5 5.9 43.2214 0.2
0.15 2.2 22.9182 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 Sun May 16 00:00:42 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days5 0.17 33.804018-42358398243-488 110.4013312-165
Lifetime (2928 days)58173 19.87 20.71162-110 488.343231-11542 389.971110-54132

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8530952 53.2
REV5702 9.8
F813543 6.1
TRN933373 5.8
0100002345 4.0
0120121224 2.1
001101730 1.3
012212718 1.2
010232709 1.2
012032619 1.1
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.852590 90.4
100 4.4 22.11318 2.3
90 19.2 11.2901 1.5
20 7.2 36.0826 1.4
95 2.4 31.6767 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 28.9111 0.2
30 9.8 20.693 0.2

TOGGLE

Toggle usage summary as of Sun May 16 00:00:53 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (4009 days)1092 0.27 47.53377-150 568.7335016-3789 3765.88 1970.5031-42841

Model Select.

ModelSelection usage summary as of Sun May 16 00:01:00 2021 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days6 0.20 58.83 29.506-234 463.28274177- 1376.67
Lifetime (2929 days)102637 35.04 43.80223-656 523.063251-11935

Top 10 Models

ModelTimes selected% selected
HKY8524648 24.0
TRN9313104 12.8
F818961 8.7
0102324383 4.3
0120123595 3.5
0122123098 3.0
0102302486 2.4
0122322436 2.4
0120322435 2.4
0011012116 2.1

Protein Model Select.

ModelSelectionP usage summary as of Sun May 16 00:01:17 2021 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days2 0.07242424-24992799279927-9927
Lifetime (4730 days)3972 0.84 46.45252-500 733.434483-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F567 14.3
JTT (Jones,Taylor,Thornton)410 10.3
BLOSUM62+F327 8.2
WAG (Whelan and Goldman)+F326 8.2
HIV (within host)+F284 7.2
IAV (Influenza A virus)+F256 6.4
WAG (Whelan and Goldman)245 6.2
IAV (Influenza A virus)228 5.7
BLOSUM62169 4.3
LG (Le and Gascuel)168 4.2

GARD

GARD usage summary as of Sun May 16 00:01:19 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days6 0.20 19.67 16.506-45 1480.17 965.50822-41301298 363.50103-3672
Lifetime (5282 days)76154 14.42 26.93182-300 2044.60111620-46625 1292.023861-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
064465 84.7
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
0-1027716 36.4
10-203031 4.0
20-302445 3.2
30-402276 3.0
40-501871 2.5
50-601976 2.6
60-701453 1.9
70-801325 1.7
80-901227 1.6
90-1001088 1.4
> 10031746 41.7
Number of breakpointsTimes found% found
023334 30.6
119254 25.3
212081 15.9
37024 9.2
44278 5.6
52946 3.9
61901 2.5
71419 1.9
8940 1.2
9762 1.0
≥ 102215 2.9

SBP

SBP usage summary as of Sun May 16 00:01:35 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days6 0.20 19.83206-40 123.3311-368 342.83 110.500-922
Lifetime (2929 days)21244 7.25 50.26252-656 21.7711-45015 606.19440-683633

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8515406 72.5
REV1315 6.2
010000565 2.7
F81503 2.4
TRN93502 2.4
0123455288 1.4
010232215 1.0
012012137 0.6
0112304567124 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-109194 43.3
10-20915 4.3
20-30804 3.8
30-40658 3.1
40-50520 2.4
50-60413 1.9
60-70361 1.7
70-80378 1.8
80-90293 1.4
90-100329 1.5
> 1007379 34.7

PARRIS

PARRIS usage summary as of Sun May 16 00:01:41 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days1 0.03181818-18243243243-243232323-23
Lifetime (5037 days)14599 2.90 20.11153-75 489.653297-11903 425.681361-48648

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858260 56.6
F811080 7.4
REV1011 6.9
TRN93777 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
0-0.12668 18.3
0.1-0.2518 3.5
0.2-0.3475 3.3
0.3-0.4373 2.6
0.4-0.5331 2.3
0.5-0.6393 2.7
0.6-0.7373 2.6
0.7-0.8360 2.5
0.8-0.9355 2.4
0.9-18753 60.0

GA Branch

GABranch usage summary as of Sun May 16 00:01:46 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00262626-26784784784-784383803838038380-38380
Last 7 days2 0.29262626-26784784784-78429748.5029748.5021117-38380
Last 30 days12 0.40 15.83 11.506-27 583.67567449-784 5813.08 372.50137-38380
Lifetime (5030 days)11878 2.36 13.75123-30 522.533339-11628 5655.5215191-889396

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858605 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
24314 36.3
34021 33.9
42239 18.8
5780 6.6
6238 2.0
7119 1.0
840 0.3
928 0.2

CMS

CMS usage summary as of Sun May 16 00:01:52 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days2 0.07252518-32 591.50 591.50227-956297829781741-4215
Lifetime (4121 days)3295 0.80 33.69243-120 571.883467-1127621130.81406659-3262277

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10192 5.8
10-20151 4.6
20-30193 5.9
30-40223 6.8
40-50249 7.6
50-60180 5.5
60-70177 5.4
70-80129 3.9
80-90178 5.4
90-100111 3.4
> 1001512 45.9
Number of rate classesTimes found% found
10 0.0
22065 62.7
3722 21.9
4283 8.6
5121 3.7
652 1.6
715 0.5
82 0.1
91 0.0
≥ 1034 1.0

DEPS

DEPS usage summary as of Sun May 16 00:01:54 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (4000 days)3614 0.90 35.76313-100 824.61 536.509-11100 485.611442-31585

Subtyping

SCUEAL usage summary as of Sun May 16 00:01:57 2021 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days70817081.00 90.8040-500
Last 7 days70811011.57 90.8040-500
Last 30 days7081236.03 90.8040-500
Lifetime (4335 days)8385 1.93 94.0750-500

Top 10 Subtypes (out of 788778 sequences)

SubtypesTimes found% found
B311874 39.5
C152357 19.3
G51493 6.5
A146609 5.9
Complex32866 4.2
AE20778 2.6
D19700 2.5
CRF1412916 1.6
F112367 1.6
B,C recombinant9827 1.2

Coevolution

BGM usage summary as of Sun May 16 00:02:01 2021 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (2929 days)8881 3.03 65.10300-1033 2.25 0.98 0.01-263 2866.47920-2900666

UCSD Viral Evolution Group 2004-2021