Datamonkey.org usage statistics

SLAC

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

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 0

Last 30 days 0

Lifetime (4026 days) 92479 22.97 53.07 25 3-684 490.95 325 1-11903 21.25 6.16 0.16- 7571.98

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	0
Last 30 days	0
Lifetime (4026 days)	92479	22.97	53.07	25	3-684	490.95	325	1-11903	21.25	6.16	0.16- 7571.98

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 47511 51.4
TRN93 13462 14.6
REV 9543 10.3
F81 4265 4.6
010230 1079 1.2
012012 1076 1.2
012212 1060 1.1
010232 1010 1.1
012232 856 0.9
012032 760 0.8

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 0.6 16.2 77137 83.4
0.05 0.5 14.1 11486 12.4
0.2 0.9 18.4 1381 1.5
0.25 2.2 24.8 776 0.8
0.5 4.3 55.2 659 0.7
0.01 0.8 9.6 540 0.6
0.15 2.2 15.2 115 0.1
0.3 0.2 18.1 51 0.1
0.0024 0.0 2.3 45 0.0
0.0048 0.0 0.5 33 0.0

FEL

FEL usage summary as of Mon Nov 29 00:00:15 2021 PST.

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 31 4.43 22.29 10 4-186 516.16 456 121-2047 28.03 17 5-144

Last 30 days 92 3.07 28.66 11 3-375 473.12 324 40-4401 47.84 17 2-1294

Lifetime (3126 days) 104295 33.36 44.57 24 3-787 488.19 325 1-11276 182.35 46 0-51470

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	31	4.43	22.29	10	4-186	516.16	456	121-2047	28.03	17	5-144
Last 30 days	92	3.07	28.66	11	3-375	473.12	324	40-4401	47.84	17	2-1294
Lifetime (3126 days)	104295	33.36	44.57	24	3-787	488.19	325	1-11276	182.35	46	0-51470

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 47506 45.5
REV 13388 12.8
TRN93 10164 9.7
F81 5463 5.2
010000 3929 3.8
010232 2094 2.0
012012 1584 1.5
012212 1405 1.3
010230 1270 1.2
012032 1005 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 23.9 84365 80.9
0.05 0.9 19.1 15402 14.8
0.2 2.1 29.7 2137 2.0
0.25 3.1 31.9 942 0.9
0.01 0.4 14.6 524 0.5
0.5 6.0 43.1 215 0.2
0.15 2.2 22.9 182 0.2
0.0024 0.0 7.0 102 0.1
0.3 1.2 23.3 64 0.1
0.06 0.3 22.5 60 0.1

REL

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

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 2 2.00 10 10 8-12 430 430 237-623 35 35 13-57

Last 7 days 2 0.29 10 10 8-12 430 430 237-623 35 35 13-57

Last 30 days 9 0.30 17 8 5-72 313.67 237 40-623 29.67 18 2-93

Lifetime (3125 days) 58320 18.66 20.71 16 2-110 488.30 323 1-11542 389.28 111 0-54132

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	2	2.00	10	10	8-12	430	430	237-623	35	35	13-57
Last 7 days	2	0.29	10	10	8-12	430	430	237-623	35	35	13-57
Last 30 days	9	0.30	17	8	5-72	313.67	237	40-623	29.67	18	2-93
Lifetime (3125 days)	58320	18.66	20.71	16	2-110	488.30	323	1-11542	389.28	111	0-54132

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 31038 53.2
REV 5722 9.8
F81 3552 6.1
TRN93 3374 5.8
010000 2345 4.0
012012 1240 2.1
001101 730 1.3
012212 720 1.2
010232 709 1.2
012032 623 1.1

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

50 4.3 27.8 52714 90.4
100 4.4 22.1 1322 2.3
90 19.2 11.2 901 1.5
20 7.2 36.0 826 1.4
95 2.4 31.6 783 1.3
10 5.8 31.7 750 1.3
40 2.5 24.4 145 0.2
25 7.8 34.7 115 0.2
80 3.0 28.9 111 0.2
30 9.8 20.6 93 0.2

TOGGLE

Toggle usage summary as of Mon Nov 29 00:00:35 2021 PST.

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 0

Last 30 days 0

Lifetime (4206 days) 1092 0.26 47.53 37 7-150 568.73 350 16-3789 3765.88 1970.50 31-42841

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	0
Last 30 days	0
Lifetime (4206 days)	1092	0.26	47.53	37	7-150	568.73	350	16-3789	3765.88	1970.50	31-42841

Model Select.

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

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 14 2.00 23.79 21 5-80 491.17 566 162.33-888

Last 30 days 41 1.37 58.34 21 3-484 601.49 383 75- 2757.67

Lifetime (3126 days) 102858 32.90 43.80 22 3-656 523.34 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	14	2.00	23.79	21	5-80	491.17	566	162.33-888
Last 30 days	41	1.37	58.34	21	3-484	601.49	383	75- 2757.67
Lifetime (3126 days)	102858	32.90	43.80	22	3-656	523.34	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 24705 24.0
TRN93 13118 12.8
F81 9010 8.8
010232 4386 4.3
012012 3619 3.5
012212 3103 3.0
010230 2487 2.4
012032 2440 2.4
012232 2437 2.4
001101 2120 2.1

Model	Times selected	% selected
HKY85	24705	24.0
TRN93	13118	12.8
F81	9010	8.8
010232	4386	4.3
012012	3619	3.5
012212	3103	3.0
010230	2487	2.4
012032	2440	2.4
012232	2437	2.4
001101	2120	2.1

Protein Model Select.

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

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 2 2.00 5 5 5-5 1277 1277 1277-1277

Last 7 days 24 3.43 9.75 10 5-15 440.42 367 153-1277

Last 30 days 57 1.90 23.61 10 3-413 792.75 420 75-9880

Lifetime (4927 days) 4150 0.84 46.22 25 2-500 984.71 459 3-18120

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	2	2.00	5	5	5-5	1277	1277	1277-1277
Last 7 days	24	3.43	9.75	10	5-15	440.42	367	153-1277
Last 30 days	57	1.90	23.61	10	3-413	792.75	420	75-9880
Lifetime (4927 days)	4150	0.84	46.22	25	2-500	984.71	459	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 570 13.7
JTT (Jones,Taylor,Thornton) 410 9.9
HIV (within host)+F 345 8.3
WAG (Whelan and Goldman)+F 341 8.2
BLOSUM62+F 338 8.1
IAV (Influenza A virus)+F 320 7.7
WAG (Whelan and Goldman) 245 5.9
IAV (Influenza A virus) 228 5.5
HIV (between hosts)+F 179 4.3
BLOSUM62 170 4.1

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)+F	570	13.7
JTT (Jones,Taylor,Thornton)	410	9.9
HIV (within host)+F	345	8.3
WAG (Whelan and Goldman)+F	341	8.2
BLOSUM62+F	338	8.1
IAV (Influenza A virus)+F	320	7.7
WAG (Whelan and Goldman)	245	5.9
IAV (Influenza A virus)	228	5.5
HIV (between hosts)+F	179	4.3
BLOSUM62	170	4.1

GARD

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

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 17 2.43 29.88 24 19-80 963.24 1080 486-1095 312.06 221 109-802

Last 30 days 41 1.37 33.46 26 3-104 2621.41 1080 468-15378 805.17 448 109-3615

Lifetime (5479 days) 76328 13.93 26.95 18 2-300 2046.44 1116 20-46625 1291.97 386 1-272974

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	17	2.43	29.88	24	19-80	963.24	1080	486-1095	312.06	221	109-802
Last 30 days	41	1.37	33.46	26	3-104	2621.41	1080	468-15378	805.17	448	109-3615
Lifetime (5479 days)	76328	13.93	26.95	18	2-300	2046.44	1116	20-46625	1291.97	386	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	64639	84.7
HKY85	5991	7.8
010000	860	1.1
REV	830	1.1
TRN93	558	0.7
F81	520	0.7
010232	226	0.3
012212	218	0.3
010230	182	0.2
012232	144	0.2

delta AIC range	Times found	% found
0-10	27809	36.4
10-20	3035	4.0
20-30	2446	3.2
30-40	2277	3.0
40-50	1873	2.5
50-60	1980	2.6
60-70	1457	1.9
70-80	1325	1.7
80-90	1228	1.6
90-100	1088	1.4
> 100	31810	41.7

Number of breakpoints	Times found	% found
0	23416	30.7
1	19302	25.3
2	12097	15.8
3	7039	9.2
4	4284	5.6
5	2949	3.9
6	1903	2.5
7	1419	1.9
8	940	1.2
9	764	1.0
≥ 10	2215	2.9

SBP

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

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 2 2.00 5 5 5-5 12 12 12-12 3.50 3.50 3-4

Last 7 days 11 1.57 12.91 10 5-26 3 1 1-12 46.27 30 3-160

Last 30 days 35 1.17 73.03 38 5-286 3.74 1 1-45 1750.83 99 1-26072

Lifetime (3126 days) 21400 6.85 50.77 25 2-656 21.78 1 1-45015 700.82 45 0-683633

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	2	2.00	5	5	5-5	12	12	12-12	3.50	3.50	3-4
Last 7 days	11	1.57	12.91	10	5-26	3	1	1-12	46.27	30	3-160
Last 30 days	35	1.17	73.03	38	5-286	3.74	1	1-45	1750.83	99	1-26072
Lifetime (3126 days)	21400	6.85	50.77	25	2-656	21.78	1	1-45015	700.82	45	0-683633

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	15518	72.5
REV	1315	6.1
010000	565	2.6
F81	503	2.4
TRN93	502	2.3
0123455	318	1.5
010232	215	1.0
012012	137	0.6
0112304567	127	0.6
010230	105	0.5

IC improvement range	Times found	% found
0-10	9238	43.2
10-20	918	4.3
20-30	807	3.8
30-40	658	3.1
40-50	528	2.5
50-60	416	1.9
60-70	361	1.7
70-80	380	1.8
80-90	295	1.4
90-100	329	1.5
> 100	7470	34.9

PARRIS

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

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 0

Last 30 days 1 0.03 21 21 21-21 156 156 156-156 40 40 40-40

Lifetime (5234 days) 14659 2.80 20.08 15 3-75 491.36 329 7-11903 424.63 136 1-48648

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	0
Last 30 days	1	0.03	21	21	21-21	156	156	156-156	40	40	40-40
Lifetime (5234 days)	14659	2.80	20.08	15	3-75	491.36	329	7-11903	424.63	136	1-48648

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8318	56.7
F81	1080	7.4
REV	1011	6.9
TRN93	777	5.3
010000	429	2.9
012012	262	1.8
001101	166	1.1
012212	155	1.1
012032	137	0.9
010230	125	0.9

p-values range	Times found	% found
0-0.1	2673	18.2
0.1-0.2	518	3.5
0.2-0.3	478	3.3
0.3-0.4	373	2.5
0.4-0.5	332	2.3
0.5-0.6	393	2.7
0.6-0.7	374	2.6
0.7-0.8	361	2.5
0.8-0.9	355	2.4
0.9-1	8802	60.0

GA Branch

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

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 1 0.14 8 8 8-8 623 623 623-623 336 336 336-336

Last 30 days 4 0.13 19.75 23 8-25 272.75 156 156-623 1098.75 1208 336-1643

Lifetime (5227 days) 11890 2.27 13.75 12 3-30 522.45 333 9-11628 5652.32 1519 1-889396

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	1	0.14	8	8	8-8	623	623	623-623	336	336	336-336
Last 30 days	4	0.13	19.75	23	8-25	272.75	156	156-623	1098.75	1208	336-1643
Lifetime (5227 days)	11890	2.27	13.75	12	3-30	522.45	333	9-11628	5652.32	1519	1-889396

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8617	72.5
REV	614	5.2
010000	568	4.8
F81	415	3.5
TRN93	285	2.4
012012	131	1.1
001101	107	0.9
012212	64	0.5
010012	63	0.5
000010	60	0.5

the number of dN/dS classes range	Times found	% found
1	99	0.8
2	4318	36.3
3	4025	33.9
4	2241	18.8
5	782	6.6
6	238	2.0
7	119	1.0
8	40	0.3
9	28	0.2

CMS

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

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 1 0.14 14 14 14-14 483 483 483-483 3993 3993 3993-3993

Last 30 days 5 0.17 20.20 21 14-25 298.20 156 156-540 2976.80 2578 1630-4973

Lifetime (4318 days) 3337 0.77 33.60 24 3-120 571.83 348 7-11276 21063.54 4074 59-3262277

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	1	0.14	14	14	14-14	483	483	483-483	3993	3993	3993-3993
Last 30 days	5	0.17	20.20	21	14-25	298.20	156	156-540	2976.80	2578	1630-4973
Lifetime (4318 days)	3337	0.77	33.60	24	3-120	571.83	348	7-11276	21063.54	4074	59-3262277

Distribution of mBIC improvement

Number of inferred rate classes

mBIC improvement range	Times found	% found
0-10	193	5.8
10-20	152	4.6
20-30	194	5.8
30-40	226	6.8
40-50	251	7.5
50-60	184	5.5
60-70	179	5.4
70-80	130	3.9
80-90	179	5.4
90-100	111	3.3
> 100	1538	46.1

Number of rate classes	Times found	% found
1	0	0.0
2	2082	62.4
3	738	22.1
4	288	8.6
5	123	3.7
6	53	1.6
7	16	0.5
8	2	0.1
9	1	0.0
≥ 10	34	1.0

DEPS

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

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 2 2.00 5 5 5-5 1277 1277 1277-1277 4.50 4.50 4-5

Last 7 days 2 0.29 5 5 5-5 1277 1277 1277-1277 4.50 4.50 4-5

Last 30 days 34 1.13 12.65 6 3-76 1364.76 1004 75-9880 41.38 6 2-628

Lifetime (4197 days) 3757 0.90 35.80 31 3-100 1077.48 556 9-11100 474.27 141 2-31585

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	2	2.00	5	5	5-5	1277	1277	1277-1277	4.50	4.50	4-5
Last 7 days	2	0.29	5	5	5-5	1277	1277	1277-1277	4.50	4.50	4-5
Last 30 days	34	1.13	12.65	6	3-76	1364.76	1004	75-9880	41.38	6	2-628
Lifetime (4197 days)	3757	0.90	35.80	31	3-100	1077.48	556	9-11100	474.27	141	2-31585

Subtyping

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

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 7225 7225.00 89.67 4 0-500

Last 7 days 7225 1032.14 89.67 4 0-500

Last 30 days 7225 240.83 89.67 4 0-500

Lifetime (4532 days) 8529 1.88 93.06 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	7225	7225.00	89.67	4	0-500
Last 7 days	7225	1032.14	89.67	4	0-500
Last 30 days	7225	240.83	89.67	4	0-500
Lifetime (4532 days)	8529	1.88	93.06	5	0-500

Top 10 Subtypes (out of 793722 sequences)

Subtypes Times found % found

B 313739 39.5

C 152854 19.3

G 51806 6.5

A1 47049 5.9

Complex 33265 4.2

AE 20792 2.6

D 19871 2.5

CRF14 12936 1.6

F1 12639 1.6

B,C recombinant 9851 1.2

Subtypes	Times found	% found
B	313739	39.5
C	152854	19.3
G	51806	6.5
A1	47049	5.9
Complex	33265	4.2
AE	20792	2.6
D	19871	2.5
CRF14	12936	1.6
F1	12639	1.6
B,C recombinant	9851	1.2

Coevolution

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

Timeframe Analyses Sites Interacting pairs/site CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 0

Last 30 days 0

Lifetime (3126 days) 8881 2.84 65.10 30 0-1033 2.25 0.98 0.01-263 2866.47 92 0-2900666

Timeframe	Analyses	Sites	Interacting pairs/site	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	0
Last 30 days	0
Lifetime (3126 days)	8881	2.84	65.10	30	0-1033	2.25	0.98	0.01-263	2866.47	92	0-2900666

UCSD Viral Evolution Group 2004-2021