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SLAC

SLAC usage summary as of Mon Feb 19 00:00:01 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days6 6.00 247.8328942-289 640.83585585-920 51.34 48.55 16.65- 73.62
Last 7 days130 18.57 56.95113-498 541.5049831-4818 11.45 1.48 0.34- 134.17
Last 30 days850 28.33 42.05223-498 579.2135017-5316 9.41 2.86 0.26- 233.84
Lifetime (2647 days)85358 32.25 51.83253-684 485.903251-11903 21.72 6.25 0.16- 7571.98

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8544305 51.9
TRN9312659 14.8
REV9204 10.8
F813741 4.4
010232964 1.1
010230942 1.1
012212876 1.0
012012768 0.9
012232703 0.8
010000654 0.8
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 0.6 16.171680 84.0
0.05 0.6 14.710285 12.0
0.2 0.9 17.11226 1.4
0.25 2.3 25.3668 0.8
0.5 4.4 55.1552 0.6
0.01 0.8 9.4517 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 Feb 19 00:00:12 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00424242-42920920920-920167167167-167
Last 7 days48 6.86 57.35453-325 556.12362107-3551 120.567411-702
Last 30 days430 14.33 46.08333-498 727.30 472.5017-4818 119.59523-1554
Lifetime (1747 days)96378 55.17 44.17243-787 478.023251-11276 141.48440-26278

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY8543472 45.1
REV12834 13.3
TRN939430 9.8
F814721 4.9
0100003907 4.1
0102322007 2.1
0120121356 1.4
0122121293 1.3
0102301173 1.2
001101908 0.9
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 24.278051 81.0
0.05 0.9 19.214396 14.9
0.2 2.2 28.91856 1.9
0.25 3.3 32.7805 0.8
0.01 0.4 14.3484 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 Feb 19 00:00:24 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00424242-42920920920-920452452452-452
Last 7 days11 1.57 21.91213-42 486.09434211-920 304.368716-1888
Last 30 days150 5.00 20.69163-69 791.1147552-4818 333.49642-10225
Lifetime (1746 days)53784 30.80 20.50152-110 480.403181-10798 360.881080-39109

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY8528553 53.1
REV5554 10.3
TRN933114 5.8
F813046 5.7
0100002327 4.3
0120121009 1.9
001101697 1.3
010232675 1.3
012212652 1.2
012032516 1.0
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.3 27.548554 90.3
100 4.2 22.61279 2.4
90 19.4 11.1890 1.7
20 7.2 36.2789 1.5
10 5.8 31.9728 1.4
95 2.4 27.9620 1.2
40 2.5 24.5144 0.3
80 3.1 28.1102 0.2
30 10.2 20.689 0.2
25 2.5 38.279 0.1

TOGGLE

Toggle usage summary as of Mon Feb 19 00:00:29 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days0
Last 30 days0
Lifetime (2827 days)1032 0.37 48.63397-150 570.1234616-3789 3856.16203931-42841

Model Select.

ModelSelection usage summary as of Mon Feb 19 00:00:30 2018 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days7 7.00 142.144222-289 593.57585280-920
Last 7 days82 11.71 82.90463-498 581.2347352-3551
Last 30 days791 26.37 43.95243-498 571.2238052-4818
Lifetime (1747 days)92989 53.23 41.32223-656 514.733251-11935

Top 10 Models

ModelTimes selected% selected
HKY8522406 24.1
TRN9312256 13.2
F818217 8.8
0102324140 4.5
0120122977 3.2
0122122739 2.9
0102302197 2.4
0120322059 2.2
0122322030 2.2
0011011934 2.1

Protein Model Select.

ModelSelectionP usage summary as of Mon Feb 19 00:00:38 2018 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days6 0.86 61.33563-1051052562210-3551
Last 30 days22 0.73 40.23203-134 603.68560130-3551
Lifetime (3548 days)3710 1.05 45.53252-499 644.274403-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)+F544 14.7
JTT (Jones,Taylor,Thornton)397 10.7
BLOSUM62+F310 8.4
WAG (Whelan and Goldman)+F305 8.2
WAG (Whelan and Goldman)238 6.4
IAV (Influenza A virus)+F234 6.3
HIV (within host)+F228 6.1
IAV (Influenza A virus)215 5.8
BLOSUM62163 4.4
LG (Le and Gascuel)148 4.0

GARD

GARD usage summary as of Mon Feb 19 00:00:40 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days1 1.00163163163-163426042604260-4260216121612161-2161
Last 7 days64 9.14 31.2383-173 3158.62135993-12000 1365.98 627.5050-5652
Last 30 days280 9.33 33.70 21.503-173 2270.7096393-15948 1081.0641750-5652
Lifetime (4100 days)73246 17.86 26.77182-300 2030.99111120-46625 1270.043721-272974

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
061557 84.0
HKY855991 8.2
010000860 1.2
REV830 1.1
TRN93558 0.8
F81520 0.7
010232226 0.3
012212218 0.3
010230182 0.2
012232144 0.2
delta AIC rangeTimes found% found
0-1026553 36.3
10-202920 4.0
20-302342 3.2
30-402197 3.0
40-501791 2.4
50-601929 2.6
60-701386 1.9
70-801291 1.8
80-901191 1.6
90-1001056 1.4
> 10030590 41.8
Number of breakpointsTimes found% found
022296 30.4
118570 25.4
211597 15.8
36726 9.2
44089 5.6
52832 3.9
61844 2.5
71392 1.9
8928 1.3
9757 1.0
≥ 102215 3.0

SBP

SBP usage summary as of Mon Feb 19 00:00:48 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days2 2.00222222-22111-1 38.50 38.5029-48
Last 7 days10 1.43 41.60224-173 13.2011-58 172.40495-935
Last 30 days28 0.93 48.82 25.503-393 16.7931-107 296.50 51.502-3945
Lifetime (1747 days)20055 11.48 48.43242-656 21.5311-45015 473.08400-279793

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY8514360 71.6
REV1311 6.5
010000565 2.8
TRN93500 2.5
F81500 2.5
0123455224 1.1
010232215 1.1
012012137 0.7
0112304567112 0.6
010230105 0.5
IC improvement rangeTimes found% found
0-108651 43.1
10-20885 4.4
20-30757 3.8
30-40615 3.1
40-50499 2.5
50-60391 1.9
60-70349 1.7
70-80363 1.8
80-90278 1.4
90-100299 1.5
> 1006968 34.7

PARRIS

PARRIS usage summary as of Mon Feb 19 00:00:51 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days3 0.43 23.672422-25 292.33256187-43417018676-248
Last 30 days18 0.60 31.22269-69 462.72321134-2411 627.61 185.5064-4095
Lifetime (3855 days)14008 3.63 20.29153-75 484.163277-11903 418.161381-35284

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY857864 56.1
F811045 7.5
REV994 7.1
TRN93730 5.2
010000429 3.1
012012250 1.8
001101166 1.2
012212153 1.1
012032127 0.9
010230119 0.8
p-values rangeTimes found% found
0-0.12583 18.4
0.1-0.2492 3.5
0.2-0.3443 3.2
0.3-0.4341 2.4
0.4-0.5321 2.3
0.5-0.6369 2.6
0.6-0.7356 2.5
0.7-0.8346 2.5
0.8-0.9341 2.4
0.9-18416 60.1

GA Branch

GABranch usage summary as of Mon Feb 19 00:00:53 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days2 0.29252525-25200200200-200734773473823-10871
Last 30 days7 0.23202512-26 340.86200145-837 3172.141795695-10871
Lifetime (3848 days)11551 3.00 13.73123-30 514.403299-11628 5307.0515061-636439

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY858290 71.8
REV611 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
199 0.9
24233 36.6
33911 33.9
42156 18.7
5756 6.5
6227 2.0
7111 1.0
835 0.3
923 0.2

CMS

CMS usage summary as of Mon Feb 19 00:00:54 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days3 0.43 67.678425-94 218.67252148-256398537293043-5183
Last 30 days10 0.33 52.60495-102 271.30 284.5099-56617933.207234237-46175
Lifetime (2939 days)3055 1.04 33.82243-120 536.253327-1127617896.50394759-2971964

Distribution of mBIC improvementNumber of inferred rate classes
mBIC improvement rangeTimes found% found
0-10182 6.0
10-20139 4.5
20-30185 6.1
30-40211 6.9
40-50239 7.8
50-60172 5.6
60-70169 5.5
70-80126 4.1
80-90165 5.4
90-100107 3.5
> 1001360 44.5
Number of rate classesTimes found% found
10 0.0
21946 63.7
3663 21.7
4251 8.2
5100 3.3
645 1.5
714 0.5
82 0.1
90 0.0
≥ 1034 1.1

DEPS

DEPS usage summary as of Mon Feb 19 00:00:54 2018 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days4 0.57655656-92 473.50560210-564 152.5014079-251
Last 30 days17 0.57 40.35408-92 337.24210135-759 216.248810-1622
Lifetime (2818 days)2714 0.96 32.01243-100 578.874329-11100 436.011002-31585

Subtyping

SCUEAL usage summary as of Mon Feb 19 00:00:55 2018 PST.

Timeframe Analyses Sequences
TotalPer 24 hrsMeanMedianRange
Last 1 days56765676.00 79.7940-500
Last 7 days5676810.86 79.7940-500
Last 30 days5676189.20 79.7940-500
Lifetime (3153 days)6980 2.21 85.7850-500

Top 10 Subtypes (out of 598729 sequences)

SubtypesTimes found% found
B230270 38.5
C106571 17.8
G42790 7.1
A138906 6.5
Complex24978 4.2
AE16802 2.8
D16717 2.8
CRF1411526 1.9
F19256 1.5
B,C recombinant7739 1.3

Coevolution

BGM usage summary as of Mon Feb 19 00:00:56 2018 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days3 0.43 87.671303-130 2.69 3.541- 3.541890222797220-287344
Last 30 days10 0.33 105.501213-130 3.25 3.541- 4.59215095.502835330-370755
Lifetime (1747 days)8686 4.97 64.74300-1033 2.27 0.98 0.01-263 2858.90960-2900666

UCSD Viral Evolution Group 2004-2018