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SLAC

SLAC usage summary as of Mon Nov 29 00:00:01 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (4026 days)92479 22.97 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 Mon Nov 29 00:00:15 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days31 4.43 22.29104-186 516.16456121-2047 28.03175-144
Last 30 days92 3.07 28.66113-375 473.1232440-4401 47.84172-1294
Lifetime (3126 days)104295 33.36 44.57243-787 488.193251-11276 182.35460-51470

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8547506 45.5
REV13388 12.8
TRN9310164 9.7
F815463 5.2
0100003929 3.8
0102322094 2.0
0120121584 1.5
0122121405 1.3
0102301270 1.2
0120321005 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 23.984365 80.9
0.05 0.9 19.115402 14.8
0.2 2.1 29.72137 2.0
0.25 3.1 31.9942 0.9
0.01 0.4 14.6524 0.5
0.5 6.0 43.1215 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 Mon Nov 29 00:00:29 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days2 2.0010108-12430430237-623353513-57
Last 7 days2 0.2910108-12430430237-623353513-57
Last 30 days9 0.301785-72 313.6723740-623 29.67182-93
Lifetime (3125 days)58320 18.66 20.71162-110 488.303231-11542 389.281110-54132

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8531038 53.2
REV5722 9.8
F813552 6.1
TRN933374 5.8
0100002345 4.0
0120121240 2.1
001101730 1.3
012212720 1.2
010232709 1.2
012032623 1.1
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.852714 90.4
100 4.4 22.11322 2.3
90 19.2 11.2901 1.5
20 7.2 36.0826 1.4
95 2.4 31.6783 1.3
10 5.8 31.7750 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 Mon Nov 29 00:00:35 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (4206 days)1092 0.26 47.53377-150 568.7335016-3789 3765.88 1970.5031-42841

Model Select.

ModelSelection usage summary as of Mon Nov 29 00:00:37 2021 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days14 2.00 23.79215-80 491.17566 162.33-888
Last 30 days41 1.37 58.34213-484 601.4938375- 2757.67
Lifetime (3126 days)102858 32.90 43.80223-656 523.343251-11935

Top 10 Models

ModelTimes selected% selected
HKY8524705 24.0
TRN9313118 12.8
F819010 8.8
0102324386 4.3
0120123619 3.5
0122123103 3.0
0102302487 2.4
0120322440 2.4
0122322437 2.4
0011012120 2.1

Protein Model Select.

ModelSelectionP usage summary as of Mon Nov 29 00:00:47 2021 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days2 2.00555-5127712771277-1277
Last 7 days24 3.43 9.75105-15 440.42367153-1277
Last 30 days57 1.90 23.61103-413 792.7542075-9880
Lifetime (4927 days)4150 0.84 46.22252-500 984.714593-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F570 13.7
JTT (Jones,Taylor,Thornton)410 9.9
HIV (within host)+F345 8.3
WAG (Whelan and Goldman)+F341 8.2
BLOSUM62+F338 8.1
IAV (Influenza A virus)+F320 7.7
WAG (Whelan and Goldman)245 5.9
IAV (Influenza A virus)228 5.5
HIV (between hosts)+F179 4.3
BLOSUM62170 4.1

GARD

GARD usage summary as of Mon Nov 29 00:00:49 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days17 2.43 29.882419-80 963.241080486-1095 312.06221109-802
Last 30 days41 1.37 33.46263-104 2621.411080468-15378 805.17448109-3615
Lifetime (5479 days)76328 13.93 26.95182-300 2046.44111620-46625 1291.973861-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
064639 84.7
HKY855991 7.8
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
0-1027809 36.4
10-203035 4.0
20-302446 3.2
30-402277 3.0
40-501873 2.5
50-601980 2.6
60-701457 1.9
70-801325 1.7
80-901228 1.6
90-1001088 1.4
> 10031810 41.7
Number of breakpointsTimes found% found
023416 30.7
119302 25.3
212097 15.8
37039 9.2
44284 5.6
52949 3.9
61903 2.5
71419 1.9
8940 1.2
9764 1.0
≥ 102215 2.9

SBP

SBP usage summary as of Mon Nov 29 00:00:58 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days2 2.00555-5121212-12 3.50 3.503-4
Last 7 days11 1.57 12.91105-26311-12 46.27303-160
Last 30 days35 1.17 73.03385-286 3.7411-45 1750.83991-26072
Lifetime (3126 days)21400 6.85 50.77252-656 21.7811-45015 700.82450-683633

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8515518 72.5
REV1315 6.1
010000565 2.6
F81503 2.4
TRN93502 2.3
0123455318 1.5
010232215 1.0
012012137 0.6
0112304567127 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-109238 43.2
10-20918 4.3
20-30807 3.8
30-40658 3.1
40-50528 2.5
50-60416 1.9
60-70361 1.7
70-80380 1.8
80-90295 1.4
90-100329 1.5
> 1007470 34.9

PARRIS

PARRIS usage summary as of Mon Nov 29 00:01:02 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days1 0.03212121-21156156156-156404040-40
Lifetime (5234 days)14659 2.80 20.08153-75 491.363297-11903 424.631361-48648

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858318 56.7
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
0-0.12673 18.2
0.1-0.2518 3.5
0.2-0.3478 3.3
0.3-0.4373 2.5
0.4-0.5332 2.3
0.5-0.6393 2.7
0.6-0.7374 2.6
0.7-0.8361 2.5
0.8-0.9355 2.4
0.9-18802 60.0

GA Branch

GABranch usage summary as of Mon Nov 29 00:01:04 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14888-8623623623-623336336336-336
Last 30 days4 0.13 19.75238-25 272.75156156-623 1098.751208336-1643
Lifetime (5227 days)11890 2.27 13.75123-30 522.453339-11628 5652.3215191-889396

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858617 72.5
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
24318 36.3
34025 33.9
42241 18.8
5782 6.6
6238 2.0
7119 1.0
840 0.3
928 0.2

CMS

CMS usage summary as of Mon Nov 29 00:01:06 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14141414-14483483483-483399339933993-3993
Last 30 days5 0.17 20.202114-25 298.20156156-540 2976.8025781630-4973
Lifetime (4318 days)3337 0.77 33.60243-120 571.833487-1127621063.54407459-3262277

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10193 5.8
10-20152 4.6
20-30194 5.8
30-40226 6.8
40-50251 7.5
50-60184 5.5
60-70179 5.4
70-80130 3.9
80-90179 5.4
90-100111 3.3
> 1001538 46.1
Number of rate classesTimes found% found
10 0.0
22082 62.4
3738 22.1
4288 8.6
5123 3.7
653 1.6
716 0.5
82 0.1
91 0.0
≥ 1034 1.0

DEPS

DEPS usage summary as of Mon Nov 29 00:01:07 2021 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days2 2.00555-5127712771277-1277 4.50 4.504-5
Last 7 days2 0.29555-5127712771277-1277 4.50 4.504-5
Last 30 days34 1.13 12.6563-76 1364.76100475-9880 41.3862-628
Lifetime (4197 days)3757 0.90 35.80313-100 1077.485569-11100 474.271412-31585

Subtyping

SCUEAL usage summary as of Mon Nov 29 00:01:09 2021 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days72257225.00 89.6740-500
Last 7 days72251032.14 89.6740-500
Last 30 days7225240.83 89.6740-500
Lifetime (4532 days)8529 1.88 93.0650-500

Top 10 Subtypes (out of 793722 sequences)

SubtypesTimes found% found
B313739 39.5
C152854 19.3
G51806 6.5
A147049 5.9
Complex33265 4.2
AE20792 2.6
D19871 2.5
CRF1412936 1.6
F112639 1.6
B,C recombinant9851 1.2

Coevolution

BGM usage summary as of Mon Nov 29 00:01:11 2021 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3126 days)8881 2.84 65.10300-1033 2.25 0.98 0.01-263 2866.47920-2900666

UCSD Viral Evolution Group 2004-2021