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SLAC

SLAC usage summary as of Fri Aug 23 00:00:01 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (3197 days)92479 28.93 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 Aug 23 00:00:13 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days202 6.73 35.86283-467 561.3644852-3434 388.47 119.508-14772
Lifetime (2297 days)102041 44.42 44.30243-787 483.963251-11276 154.75450-51470

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8546116 45.2
REV13207 12.9
TRN9310031 9.8
F815253 5.1
0100003926 3.8
0102322081 2.0
0120121569 1.5
0122121383 1.4
0102301244 1.2
012032994 1.0
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.182493 80.8
0.05 0.9 19.115116 14.8
0.2 2.1 29.92110 2.1
0.25 3.1 32.5909 0.9
0.01 0.4 14.7520 0.5
0.5 5.9 43.2214 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 Fri Aug 23 00:00:27 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days219 7.30 28.65283-45 470.0644452-3434 514.293421-6741
Lifetime (2296 days)56831 24.75 20.67162-110 484.983221-10798 388.161110-54132

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8530127 53.0
REV5655 10.0
F813363 5.9
TRN933330 5.9
0100002339 4.1
0120121193 2.1
001101727 1.3
012212704 1.2
010232694 1.2
012032610 1.1
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.951397 90.4
100 4.3 22.41301 2.3
90 19.2 11.2900 1.6
20 7.2 35.9820 1.4
10 5.8 31.9746 1.3
95 2.2 30.8713 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 Fri Aug 23 00:00:33 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days1 0.03878787-87226226226-226425042504250-4250
Lifetime (3377 days)1077 0.32 47.56377-150 571.1535016-3789 3783.42197331-42841

Model Select.

ModelSelection usage summary as of Fri Aug 23 00:00:35 2019 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14212121-21566566566-566
Last 30 days202 6.73 44.82 18.503-472 655.4568425-3787
Lifetime (2297 days)100424 43.72 43.70223-656 519.663251-11935

Top 10 Models

ModelTimes selected% selected
HKY8524093 24.0
TRN9312953 12.9
F818671 8.6
0102324312 4.3
0120123484 3.5
0122123028 3.0
0102302443 2.4
0122322390 2.4
0120322387 2.4
0011012094 2.1

Protein Model Select.

ModelSelectionP usage summary as of Fri Aug 23 00:00:44 2019 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29333-3403403403-403
Last 30 days7 0.23 18.1453-42 225.4321465-403
Lifetime (4098 days)3857 0.94 46.21252-499 651.244403-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F562 14.6
JTT (Jones,Taylor,Thornton)406 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)225 5.8
BLOSUM62168 4.4
LG (Le and Gascuel)161 4.2

GARD

GARD usage summary as of Fri Aug 23 00:00:46 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days112 3.73 23.74203-94 2550.48 2428.50432-10302 2652.713615241-11209
Lifetime (4650 days)75119 16.15 26.86182-300 2035.65111620-46625 1287.303821-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
063430 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
0-1027270 36.3
10-202991 4.0
20-302421 3.2
30-402252 3.0
40-501849 2.5
50-601953 2.6
60-701427 1.9
70-801316 1.8
80-901217 1.6
90-1001081 1.4
> 10031342 41.7
Number of breakpointsTimes found% found
022936 30.5
119014 25.3
211918 15.9
36928 9.2
44224 5.6
52905 3.9
61875 2.5
71409 1.9
8934 1.2
9761 1.0
≥ 102215 2.9

SBP

SBP usage summary as of Fri Aug 23 00:00:55 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days24 0.80 165.67 121.503-472 4.3811-36 1755.75 969.500-7480
Lifetime (2297 days)20729 9.02 49.76252-656 21.8511-45015 595.57420-683633

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8514989 72.3
REV1315 6.3
010000565 2.7
F81503 2.4
TRN93502 2.4
0123455236 1.1
010232215 1.0
012012137 0.7
0112304567119 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-108986 43.3
10-20898 4.3
20-30788 3.8
30-40644 3.1
40-50508 2.5
50-60406 2.0
60-70358 1.7
70-80376 1.8
80-90282 1.4
90-100315 1.5
> 1007168 34.6

PARRIS

PARRIS usage summary as of Fri Aug 23 00:00:59 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days25 0.83 9.9694-37 295.32208106-1025 513.962856-2883
Lifetime (4405 days)14410 3.27 20.12153-75 485.803297-11903 426.831371-48648

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY858161 56.6
F811068 7.4
REV1008 7.0
TRN93757 5.3
010000429 3.0
012012255 1.8
001101166 1.2
012212155 1.1
012032128 0.9
010230125 0.9
p-values rangeTimes found% found
0-0.12627 18.2
0.1-0.2513 3.6
0.2-0.3465 3.2
0.3-0.4365 2.5
0.4-0.5331 2.3
0.5-0.6391 2.7
0.6-0.7370 2.6
0.7-0.8358 2.5
0.8-0.9354 2.5
0.9-18636 59.9

GA Branch

GABranch usage summary as of Fri Aug 23 00:01:01 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days4 0.13 16.25 16.5012-20813821533-107718851.25189122872-34709
Lifetime (4398 days)11727 2.67 13.73123-30 519.373319-11628 5595.6715201-889396

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858454 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
24285 36.5
33958 33.8
42199 18.8
5774 6.6
6234 2.0
7117 1.0
837 0.3
924 0.2

CMS

CMS usage summary as of Fri Aug 23 00:01:03 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days5 0.17 35.203532-41 1274.8013641032-153267298.405529639096-135131
Lifetime (3489 days)3194 0.92 33.72243-120 563.783407-1127620749.73404659-3262277

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
30-40217 6.8
40-50243 7.6
50-60178 5.6
60-70174 5.4
70-80128 4.0
80-90175 5.5
90-100108 3.4
> 1001453 45.5
Number of rate classesTimes found% found
10 0.0
22011 63.0
3705 22.1
4270 8.5
5108 3.4
648 1.5
715 0.5
82 0.1
91 0.0
≥ 1034 1.1

DEPS

DEPS usage summary as of Fri Aug 23 00:01:04 2019 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days36 1.20 43.14464-76 1078.2847165-4527 386.28 337.507-1245
Lifetime (3368 days)3167 0.94 34.31283-100 623.364819-11100 512.371282-31585

Subtyping

SCUEAL usage summary as of Fri Aug 23 00:01:05 2019 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days63096309.00 82.7640-500
Last 7 days6309901.29 82.7640-500
Last 30 days6309210.30 82.7640-500
Lifetime (3703 days)7613 2.06 87.7450-500

Top 10 Subtypes (out of 667940 sequences)

SubtypesTimes found% found
B260574 39.0
C115814 17.3
G46053 6.9
A141824 6.3
Complex28102 4.2
AE19795 3.0
D18899 2.8
CRF1411763 1.8
F110599 1.6
B,C recombinant9116 1.4

Coevolution

BGM usage summary as of Fri Aug 23 00:01:08 2019 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (2297 days)8881 3.87 65.10300-1033 2.25 0.98 0.01-263 2866.47920-2900666

UCSD Viral Evolution Group 2004-2019