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SLAC

SLAC usage summary as of Mon Jun 17 00:00:01 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3130 days)92479 29.55 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 Jun 17 00:00:12 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days11 11.00 33.274021-40 498.91504262-566 124.278569-304
Last 7 days82 11.71 52.51233-446 326.8331252-716 614.30 277.5017-7483
Last 30 days222 7.40 59.57233-500 555.73 344.5052-4787 1685.16 494.5012-39106
Lifetime (2230 days)101654 45.58 44.27243-787 483.353251-11276 152.41450-39106

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8545828 45.1
REV13201 13.0
TRN9310018 9.9
F815234 5.1
0100003926 3.9
0102322081 2.0
0120121563 1.5
0122121379 1.4
0102301241 1.2
012032991 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.182241 80.9
0.05 0.9 19.215024 14.8
0.2 2.1 30.02069 2.0
0.25 3.1 32.5909 0.9
0.01 0.4 14.7520 0.5
0.5 5.9 42.7212 0.2
0.15 2.5 23.5161 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 Jun 17 00:00:25 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days9 9.00 24.672318-40 365.5626253-845 811.4462084-1545
Last 7 days64 9.14 22.75235-57 270.1222753-845 1183.42112553-4219
Last 30 days111 3.70 22.57234-57 399.7127353-2103 1655.92107245-19637
Lifetime (2229 days)56473 25.34 20.64162-110 485.433221-10798 385.521100-54132

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8529865 52.9
REV5652 10.0
F813324 5.9
TRN933324 5.9
0100002336 4.1
0120121185 2.1
001101727 1.3
012212702 1.2
010232694 1.2
012032608 1.1
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.851049 90.4
100 4.2 22.41300 2.3
90 19.2 11.2900 1.6
20 7.2 36.0819 1.5
10 5.8 31.9746 1.3
95 2.2 30.8707 1.3
40 2.5 24.4145 0.3
80 3.0 28.0109 0.2
30 10.0 20.291 0.2
25 3.4 36.786 0.2

TOGGLE

Toggle usage summary as of Mon Jun 17 00:00:31 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days1 0.03282828-28343434343434-3434396539653965-3965
Lifetime (3310 days)1076 0.33 47.52377-150 571.4735016-3789 3782.98 1970.5031-42841

Model Select.

ModelSelection usage summary as of Mon Jun 17 00:00:32 2019 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days15 15.00 262.4742821-478551566469-845
Last 7 days172 24.57 211.09 187.503-499 424.4949521-845
Last 30 days391 13.03 169.161203-500 505.3146921-3434
Lifetime (2230 days)99963 44.83 43.55223-656 518.483251-11935

Top 10 Models

ModelTimes selected% selected
HKY8524034 24.0
TRN9312924 12.9
F818634 8.6
0102324305 4.3
0120123440 3.4
0122123011 3.0
0102302419 2.4
0122322379 2.4
0120322363 2.4
0011012085 2.1

Protein Model Select.

ModelSelectionP usage summary as of Mon Jun 17 00:00:40 2019 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14222222-22225225225-225
Last 30 days6 0.20 150.1712522-299 1707.671351225-3557
Lifetime (4031 days)3843 0.95 46.26252-499 652.614443-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F560 14.6
JTT (Jones,Taylor,Thornton)404 10.5
BLOSUM62+F324 8.4
WAG (Whelan and Goldman)+F320 8.3
WAG (Whelan and Goldman)244 6.3
HIV (within host)+F243 6.3
IAV (Influenza A virus)+F238 6.2
IAV (Influenza A virus)223 5.8
BLOSUM62167 4.3
LG (Le and Gascuel)161 4.2

GARD

GARD usage summary as of Mon Jun 17 00:00:42 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days4 4.00 35.254021-40 1558.5015121512-1698 881.25441408-2235
Last 7 days26 3.71 31.85243-86 1062.69124783-2130 1878.96 1024.50408-6097
Last 30 days98 3.27 33.53 23.503-161 2320.10 1324.5083-14361 2623.142439222-11590
Lifetime (4583 days)74929 16.35 26.86182-300 2034.15111320-46625 1283.433801-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
063240 84.4
HKY855991 8.0
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
0-1027223 36.3
10-202989 4.0
20-302415 3.2
30-402243 3.0
40-501848 2.5
50-601952 2.6
60-701422 1.9
70-801314 1.8
80-901216 1.6
90-1001077 1.4
> 10031230 41.7
Number of breakpointsTimes found% found
022892 30.6
118979 25.3
211895 15.9
36894 9.2
44194 5.6
52889 3.9
61869 2.5
71407 1.9
8934 1.2
9761 1.0
≥ 102215 3.0

SBP

SBP usage summary as of Mon Jun 17 00:00:51 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days15 2.14 48.67693-88 23.8711-1352871841-1314
Last 30 days56 1.87 76.80383-437 13.7111-264 3786.292191-74373
Lifetime (2230 days)20673 9.27 49.57252-656 21.7811-45015 578.44420-683633

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8514941 72.3
REV1315 6.4
010000565 2.7
F81503 2.4
TRN93502 2.4
0123455232 1.1
010232215 1.0
012012137 0.7
0112304567117 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-108952 43.3
10-20897 4.3
20-30788 3.8
30-40640 3.1
40-50508 2.5
50-60406 2.0
60-70353 1.7
70-80375 1.8
80-90282 1.4
90-100315 1.5
> 1007157 34.6

PARRIS

PARRIS usage summary as of Mon Jun 17 00:00:54 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days13 0.43 19.77184-47 551.77225107-1575 2187.15179941-4863
Lifetime (4338 days)14362 3.31 20.15153-75 486.523297-11903 426.651371-48648

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858130 56.6
F811064 7.4
REV1005 7.0
TRN93756 5.3
010000429 3.0
012012252 1.8
001101166 1.2
012212155 1.1
012032128 0.9
010230125 0.9
p-values rangeTimes found% found
0-0.12623 18.3
0.1-0.2510 3.6
0.2-0.3463 3.2
0.3-0.4365 2.5
0.4-0.5330 2.3
0.5-0.6390 2.7
0.6-0.7368 2.6
0.7-0.8357 2.5
0.8-0.9352 2.5
0.9-18604 59.9

GA Branch

GABranch usage summary as of Mon Jun 17 00:00:55 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days3 0.10 14.331312-18411429363-44127771240696313-52931
Lifetime (4331 days)11714 2.70 13.73123-30 519.203319-11628 5573.69 1520.501-889396

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858441 72.1
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
24277 36.5
33957 33.8
42199 18.8
5773 6.6
6233 2.0
7116 1.0
836 0.3
924 0.2

CMS

CMS usage summary as of Mon Jun 17 00:00:56 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29 54.50 54.5026-83221221132-310432384323828743-57733
Last 30 days4 0.13 41.50 28.5026-83 1066.25 349.50132-343431984.252846213280-57733
Lifetime (3422 days)3184 0.93 33.68243-120 556.763407-1127618863.52 4029.5059-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10184 5.8
10-20146 4.6
20-30188 5.9
30-40216 6.8
40-50243 7.6
50-60178 5.6
60-70174 5.5
70-80128 4.0
80-90175 5.5
90-100108 3.4
> 1001444 45.4
Number of rate classesTimes found% found
10 0.0
22009 63.1
3704 22.1
4266 8.4
5107 3.4
648 1.5
714 0.4
82 0.1
90 0.0
≥ 1034 1.1

DEPS

DEPS usage summary as of Mon Jun 17 00:00:57 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14111111-11525252-52102102102-102
Last 30 days4 0.13 41.503711-811105 405.5052-3557 1394.751383102-2711
Lifetime (3301 days)3129 0.95 34.18273-100 618.294819-11100 513.081262-31585

Subtyping

SCUEAL usage summary as of Mon Jun 17 00:00:58 2019 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days62016201.00 83.2840-500
Last 7 days6201885.86 83.2840-500
Last 30 days6201206.70 83.2840-500
Lifetime (3636 days)7505 2.06 88.2450-500

Top 10 Subtypes (out of 662226 sequences)

SubtypesTimes found% found
B258992 39.1
C113210 17.1
G46009 6.9
A141601 6.3
Complex27852 4.2
AE19756 3.0
D18841 2.8
CRF1411763 1.8
F110530 1.6
B,C recombinant8931 1.3

Coevolution

BGM usage summary as of Mon Jun 17 00:01:00 2019 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (2230 days)8881 3.98 65.10300-1033 2.25 0.98 0.01-263 2866.47920-2900666

UCSD Viral Evolution Group 2004-2019