Analyze your data Home Help Citations Job Queue Stats HyPhy package
Navigation Banner

SLAC

SLAC usage summary as of Mon Oct 23 00:00:01 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days5 5.00 42.204719-69 330.6025699-887 16.20 5.37 1.84- 60.89
Last 7 days204 29.14 46.32284-500 473.2033342-11276 10.35 3.98 0.45- 301.47
Last 30 days952 31.73 43.03213-500 437.7032513-11276 9.22 2.95 0.24- 402.18
Lifetime (2528 days)82531 32.65 52.02253-684 481.613251-11903 22.00 6.30 0.16- 7571.98

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8543145 52.3
TRN9312213 14.8
REV8988 10.9
F813622 4.4
010232921 1.1
010230903 1.1
012212806 1.0
012012732 0.9
010000648 0.8
012232635 0.8
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 0.6 16.069140 83.8
0.05 0.6 14.510103 12.2
0.2 0.9 17.21178 1.4
0.25 2.3 25.2665 0.8
0.01 0.8 9.5510 0.6
0.5 4.4 54.7506 0.6
0.15 2.9 14.888 0.1
0.0024 0.0 2.345 0.1
0.3 0.2 20.045 0.1
0.0048 0.0 0.533 0.0

FEL

FEL usage summary as of Mon Oct 23 00:00:12 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days12 12.00 41.674721-47 397.17256256-887 154.75 80.5058-646
Last 7 days95 13.57 53.53275-500 715.4856686-11276 185.78697-2258
Last 30 days642 21.40 53.20283-500 491.62 332.5016-11276 170.33564-4248
Lifetime (1628 days)94155 57.83 43.99243-787 472.663251-11276 140.61440-26278

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8542588 45.2
REV12644 13.4
TRN939146 9.7
F814609 4.9
0100003901 4.1
0102321970 2.1
0120121318 1.4
0122121261 1.3
0102301128 1.2
001101894 0.9
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.176129 80.9
0.05 0.9 19.114178 15.1
0.2 2.1 28.61781 1.9
0.25 3.3 32.7801 0.9
0.01 0.4 14.3482 0.5
0.5 5.6 44.7187 0.2
0.15 2.9 21.9131 0.1
0.0024 0.0 7.0102 0.1
0.3 1.2 22.363 0.1
0.0004 0.0 6.629 0.0

REL

REL usage summary as of Mon Oct 23 00:00:24 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00292929-29887887887-887614614614-614
Last 7 days31 4.43 21.65123-70 645.13603119-2880 528.4510213-5072
Last 30 days235 7.83 20.92173-70 493.9728316-2886 402.421074-27306
Lifetime (1627 days)52622 32.34 20.44152-110 475.763151-10798 358.091080-38013

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8527993 53.2
REV5444 10.3
TRN933008 5.7
F812968 5.6
0100002324 4.4
012012985 1.9
001101689 1.3
010232668 1.3
012212625 1.2
012032495 0.9
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.447431 90.1
100 4.2 22.51273 2.4
90 19.6 10.9882 1.7
20 7.3 36.2782 1.5
10 5.8 31.7719 1.4
95 2.3 27.9615 1.2
40 2.5 24.5144 0.3
80 3.2 27.199 0.2
30 10.2 20.689 0.2
25 2.5 38.279 0.2

TOGGLE

Toggle usage summary as of Mon Oct 23 00:00:30 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14383838-38299299299-299657657657-657
Last 30 days7 0.23 72.438028-105 343.86302228-464 5140.861751417-14730
Lifetime (2708 days)974 0.36 48.73397-150 568.99 341.5016-3789 3949.82 2076.5031-42841

Model Select.

ModelSelection usage summary as of Mon Oct 23 00:00:31 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days21 21.00 22.24114-76 262.1325699- 355.67
Last 7 days157 22.43 30.87143-307 532.09 334.6771-11276
Last 30 days621 20.70 47.05233-443 502.9732516-11276
Lifetime (1628 days)89979 55.27 41.27223-656 510.903251-11935

Top 10 Models

ModelTimes selected% selected
HKY8521638 24.0
TRN9311869 13.2
F818089 9.0
0102324022 4.5
0120122872 3.2
0122122638 2.9
0102302133 2.4
0011011913 2.1
0122321913 2.1
0120321903 2.1

Protein Model Select.

ModelSelectionP usage summary as of Mon Oct 23 00:00:38 2017 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days3 3.00474747-47257257257-257
Last 7 days14 2.00 65.29508-277 340.213057-661
Last 30 days32 1.07 71.12476-305 454.16 339.507-3423
Lifetime (3429 days)3634 1.06 45.53252-499 643.734403-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F537 14.8
JTT (Jones,Taylor,Thornton)394 10.8
BLOSUM62+F300 8.3
WAG (Whelan and Goldman)+F296 8.1
WAG (Whelan and Goldman)237 6.5
IAV (Influenza A virus)+F224 6.2
HIV (within host)+F219 6.0
IAV (Influenza A virus)207 5.7
BLOSUM62161 4.4
LG (Le and Gascuel)146 4.0

GARD

GARD usage summary as of Mon Oct 23 00:00:40 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days3 3.00737469-76 855.331050465-1051 772.67688490-1140
Last 7 days64 9.14 23.20164-83 2799.47 886.50117-33828 1085.27 437.5084-5651
Last 30 days205 6.83 34.83203-258 2228.10942117-33828 1565.0551161-22587
Lifetime (3981 days)72288 18.16 26.67182-300 2029.24110920-46625 1268.653681-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
060599 83.8
HKY855991 8.3
010000860 1.2
REV830 1.1
TRN93558 0.8
F81520 0.7
010232226 0.3
012212218 0.3
010230182 0.3
012232144 0.2
delta AIC rangeTimes found% found
0-1026150 36.2
10-202869 4.0
20-302315 3.2
30-402162 3.0
40-501761 2.4
50-601919 2.7
60-701365 1.9
70-801270 1.8
80-901171 1.6
90-1001045 1.4
> 10030261 41.9
Number of breakpointsTimes found% found
021953 30.4
118313 25.3
211410 15.8
36651 9.2
44050 5.6
52815 3.9
61822 2.5
71384 1.9
8920 1.3
9755 1.0
≥ 102215 3.1

SBP

SBP usage summary as of Mon Oct 23 00:00:49 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days7 7.00 21.291111-47111-136107-105
Last 7 days20 2.86 45.65137-499 9.3511-48 389.90 9.503-5959
Last 30 days112 3.73 64.96233-499 7.48 1.501-92 598.13 30.501-11394
Lifetime (1628 days)19843 12.19 48.55252-656 21.6411-45015 475.28400-279793

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8514162 71.4
REV1311 6.6
010000565 2.8
F81500 2.5
TRN93498 2.5
0123455220 1.1
010232215 1.1
012012137 0.7
0112304567111 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-108597 43.3
10-20882 4.4
20-30742 3.7
30-40600 3.0
40-50496 2.5
50-60387 2.0
60-70347 1.7
70-80353 1.8
80-90276 1.4
90-100287 1.4
> 1006876 34.7

PARRIS

PARRIS usage summary as of Mon Oct 23 00:00:52 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days5 0.71333313-44942603310-2880 1627.40351103-7121
Last 30 days42 1.40 17.62 11.503-58 562.8831213-2880 410.50 107.505-7121
Lifetime (3736 days)13861 3.71 20.26153-75 482.743267-11903 412.801371-35284

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY857762 56.0
F811042 7.5
REV987 7.1
TRN93717 5.2
010000429 3.1
012012250 1.8
001101166 1.2
012212152 1.1
012032125 0.9
010230119 0.9
p-values rangeTimes found% found
0-0.12562 18.5
0.1-0.2486 3.5
0.2-0.3441 3.2
0.3-0.4339 2.4
0.4-0.5321 2.3
0.5-0.6369 2.7
0.6-0.7352 2.5
0.7-0.8341 2.5
0.8-0.9339 2.4
0.9-18311 60.0

GA Branch

GABranch usage summary as of Mon Oct 23 00:00:53 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days4 0.57 10.25116-13224 149.50106-491 2398.25 1774.50210-5834
Last 30 days23 0.77 12.30116-28325228106-877 3167.04978210-20584
Lifetime (3729 days)11487 3.08 13.72123-30 513.393299-11628 5311.9615051-636439

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858228 71.6
REV610 5.3
010000568 4.9
F81412 3.6
TRN93280 2.4
012012131 1.1
001101107 0.9
01221264 0.6
01001263 0.5
00001060 0.5
the number of dN/dS classes rangeTimes found% found
197 0.8
24215 36.7
33889 33.9
42143 18.7
5752 6.5
6224 2.0
7109 0.9
835 0.3
923 0.2

CMS

CMS usage summary as of Mon Oct 23 00:00:54 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days3 3.00394421-524166619603-11276194527.6731131267-579203
Last 7 days3 0.43394421-524166619603-11276194527.6731131267-579203
Last 30 days20 0.67 37.30 37.507-80 1124.75 338.5032-1127648373.508855839-579203
Lifetime (2820 days)2999 1.06 33.67243-120 537.273327-1127617747.28396659-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10182 6.1
10-20136 4.5
20-30182 6.1
30-40210 7.0
40-50232 7.7
50-60164 5.5
60-70166 5.5
70-80124 4.1
80-90164 5.5
90-100106 3.5
> 1001333 44.4
Number of rate classesTimes found% found
10 0.0
21911 63.7
3650 21.7
4246 8.2
598 3.3
644 1.5
714 0.5
82 0.1
90 0.0
≥ 1034 1.1

DEPS

DEPS usage summary as of Mon Oct 23 00:00:55 2017 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00474747-47257257257-257330330330-330
Last 7 days29 4.14 86.2110013-100 341.45333211-566 2345.34169769-7311
Last 30 days43 1.43 64.631005-100 676.0933323-11100 1757.778957-7311
Lifetime (2699 days)2665 0.99 31.70243-100 580.174449-11100 436.39992-31585

Subtyping

SCUEAL usage summary as of Mon Oct 23 00:00:55 2017 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days55455545.00 79.3840-500
Last 7 days5545792.14 79.3840-500
Last 30 days5545184.83 79.3840-500
Lifetime (3034 days)6849 2.26 85.5650-500

Top 10 Subtypes (out of 586024 sequences)

SubtypesTimes found% found
B223903 38.2
C104896 17.9
G42585 7.3
A138617 6.6
Complex24566 4.2
D16648 2.8
AE16236 2.8
CRF1411516 2.0
F18600 1.5
B,C recombinant7545 1.3

Coevolution

BGM usage summary as of Mon Oct 23 00:00:57 2017 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days4 4.001677-43 0.981 0.91-1 33.5011-131
Last 7 days4 0.571677-43 0.981 0.91-1 33.5011-131
Last 30 days29 0.97 56.31161-427 1.28 0.91 0.19-6 209.5240-3336
Lifetime (1628 days)8585 5.27 64.71300-1033 2.26 0.97 0.01-263 2610.61930-2900666

UCSD Viral Evolution Group 2004-2017