Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Tue Sep 21 00:00:02 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 0

Lifetime (3957 days) 92479 23.37 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 (3957 days)	92479	23.37	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 Tue Sep 21 00:00:13 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 73 10.43 29.60 15 3-229 606.66 525 38-4402 63.82 37 3-493

Last 30 days 116 3.87 48.41 16 3-388 583.05 460.50 38-4402 99.53 28.50 2-2397

Lifetime (3057 days) 104127 34.06 44.59 24 3-787 488.22 325 1-11276 182.54 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	73	10.43	29.60	15	3-229	606.66	525	38-4402	63.82	37	3-493
Last 30 days	116	3.87	48.41	16	3-388	583.05	460.50	38-4402	99.53	28.50	2-2397
Lifetime (3057 days)	104127	34.06	44.59	24	3-787	488.22	325	1-11276	182.54	46	0-51470

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 47363 45.5
REV 13384 12.9
TRN93 10160 9.8
F81 5451 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 84203 80.9
0.05 0.9 19.1 15396 14.8
0.2 2.1 29.7 2137 2.1
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 Tue Sep 21 00:00:27 2021 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 1 1.00 7 7 7-7 385 385 385-385 23 23 23-23

Last 7 days 2 0.29 8.50 8.50 7-10 309.50 309.50 234-385 18 18 13-23

Last 30 days 8 0.27 22.50 14 3-73 489.12 309.50 63-1252 142.25 57 2-561

Lifetime (3056 days) 58299 19.08 20.71 16 2-110 488.38 323 1-11542 389.39 111 0-54132

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	1	1.00	7	7	7-7	385	385	385-385	23	23	23-23
Last 7 days	2	0.29	8.50	8.50	7-10	309.50	309.50	234-385	18	18	13-23
Last 30 days	8	0.27	22.50	14	3-73	489.12	309.50	63-1252	142.25	57	2-561
Lifetime (3056 days)	58299	19.08	20.71	16	2-110	488.38	323	1-11542	389.39	111	0-54132

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 31024 53.2
REV 5722 9.8
F81 3549 6.1
TRN93 3373 5.8
010000 2345 4.0
012012 1239 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 52693 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 Tue Sep 21 00:00:34 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 (4137 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 (4137 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 Tue Sep 21 00:00:35 2021 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 62 8.86 28.58 14 4-137 679.76 292.50 38-7094

Last 30 days 66 2.20 28.62 14 4-137 654.58 292.50 38-7094

Lifetime (3057 days) 102760 33.61 43.79 22 3-656 523.18 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	62	8.86	28.58	14	4-137	679.76	292.50	38-7094
Last 30 days	66	2.20	28.62	14	4-137	654.58	292.50	38-7094
Lifetime (3057 days)	102760	33.61	43.79	22	3-656	523.18	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 24669 24.0
TRN93 13108 12.8
F81 8990 8.7
010232 4383 4.3
012012 3617 3.5
012212 3102 3.0
010230 2487 2.4
012032 2439 2.4
012232 2437 2.4
001101 2120 2.1

Model	Times selected	% selected
HKY85	24669	24.0
TRN93	13108	12.8
F81	8990	8.7
010232	4383	4.3
012012	3617	3.5
012212	3102	3.0
010230	2487	2.4
012032	2439	2.4
012232	2437	2.4
001101	2120	2.1

Protein Model Select.

ModelSelectionP usage summary as of Tue Sep 21 00:00:45 2021 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 1 0.14 46 46 46-46 3551 3551 3551-3551

Last 30 days 41 1.37 40.15 39 4-93 9652.34 9805 3551-9812

Lifetime (4858 days) 4091 0.84 46.48 26 2-500 987.69 463 3-18120

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	1	0.14	46	46	46-46	3551	3551	3551-3551
Last 30 days	41	1.37	40.15	39	4-93	9652.34	9805	3551-9812
Lifetime (4858 days)	4091	0.84	46.48	26	2-500	987.69	463	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 567 13.9
JTT (Jones,Taylor,Thornton) 410 10.0
HIV (within host)+F 335 8.2
BLOSUM62+F 329 8.0
WAG (Whelan and Goldman)+F 326 8.0
IAV (Influenza A virus)+F 306 7.5
WAG (Whelan and Goldman) 245 6.0
IAV (Influenza A virus) 228 5.6
HIV (between hosts)+F 178 4.4
BLOSUM62 169 4.1

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)+F	567	13.9
JTT (Jones,Taylor,Thornton)	410	10.0
HIV (within host)+F	335	8.2
BLOSUM62+F	329	8.0
WAG (Whelan and Goldman)+F	326	8.0
IAV (Influenza A virus)+F	306	7.5
WAG (Whelan and Goldman)	245	6.0
IAV (Influenza A virus)	228	5.6
HIV (between hosts)+F	178	4.4
BLOSUM62	169	4.1

GARD

GARD usage summary as of Tue Sep 21 00:00:46 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 41 5.86 27.63 14 4-137 1979.63 861 114-21282 478.32 236 51-2979

Last 30 days 55 1.83 34.40 24 4-137 2700.95 918 114-21282 1001.24 312 51-5192

Lifetime (5410 days) 76271 14.10 26.95 18 2-300 2046.33 1116 20-46625 1292.43 386 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	41	5.86	27.63	14	4-137	1979.63	861	114-21282	478.32	236	51-2979
Last 30 days	55	1.83	34.40	24	4-137	2700.95	918	114-21282	1001.24	312	51-5192
Lifetime (5410 days)	76271	14.10	26.95	18	2-300	2046.33	1116	20-46625	1292.43	386	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	64582	84.7
HKY85	5991	7.9
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	27782	36.4
10-20	3032	4.0
20-30	2445	3.2
30-40	2276	3.0
40-50	1871	2.5
50-60	1977	2.6
60-70	1454	1.9
70-80	1325	1.7
80-90	1228	1.6
90-100	1088	1.4
> 100	31793	41.7

Number of breakpoints	Times found	% found
0	23399	30.7
1	19270	25.3
2	12096	15.9
3	7037	9.2
4	4283	5.6
5	2947	3.9
6	1903	2.5
7	1419	1.9
8	940	1.2
9	762	1.0
≥ 10	2215	2.9

SBP

SBP usage summary as of Tue Sep 21 00:00:56 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 0.14 119 119 119-119 9 9 9-9 932 932 932-932

Last 30 days 8 0.27 48.38 46 5-119 6 3 1-22 435 334.50 2-932

Lifetime (3057 days) 21324 6.98 50.60 25 2-656 21.79 1 1-45015 636.88 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	0
Last 7 days	1	0.14	119	119	119-119	9	9	9-9	932	932	932-932
Last 30 days	8	0.27	48.38	46	5-119	6	3	1-22	435	334.50	2-932
Lifetime (3057 days)	21324	6.98	50.60	25	2-656	21.79	1	1-45015	636.88	45	0-683633

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	15461	72.5
REV	1315	6.2
010000	565	2.6
F81	503	2.4
TRN93	502	2.4
0123455	306	1.4
010232	215	1.0
012012	137	0.6
0112304567	125	0.6
010230	105	0.5

IC improvement range	Times found	% found
0-10	9224	43.3
10-20	917	4.3
20-30	806	3.8
30-40	658	3.1
40-50	520	2.4
50-60	416	2.0
60-70	361	1.7
70-80	379	1.8
80-90	295	1.4
90-100	329	1.5
> 100	7419	34.8

PARRIS

PARRIS usage summary as of Tue Sep 21 00:00:59 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 43 6.14 10.09 10 4-30 1146.30 932 176-4283 195.51 59 7-2396

Last 30 days 44 1.47 10.75 10 4-39 1123.45 927 141-4283 192.18 58 7-2396

Lifetime (5165 days) 14651 2.84 20.09 15 3-75 491.54 329 7-11903 424.86 136 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	43	6.14	10.09	10	4-30	1146.30	932	176-4283	195.51	59	7-2396
Last 30 days	44	1.47	10.75	10	4-39	1123.45	927	141-4283	192.18	58	7-2396
Lifetime (5165 days)	14651	2.84	20.09	15	3-75	491.54	329	7-11903	424.86	136	1-48648

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8312	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	360	2.5
0.8-0.9	355	2.4
0.9-1	8795	60.0

GA Branch

GABranch usage summary as of Tue Sep 21 00:01:01 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 1 0.03 24 24 24-24 233 233 233-233 4303 4303 4303-4303

Lifetime (5158 days) 11883 2.30 13.75 12 3-30 522.49 333 9-11628 5653.93 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	0
Last 30 days	1	0.03	24	24	24-24	233	233	233-233	4303	4303	4303-4303
Lifetime (5158 days)	11883	2.30	13.75	12	3-30	522.49	333	9-11628	5653.93	1519	1-889396

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8610	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	4316	36.3
3	4022	33.8
4	2241	18.9
5	780	6.6
6	238	2.0
7	119	1.0
8	40	0.3
9	28	0.2

CMS

CMS usage summary as of Tue Sep 21 00:01:03 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 4 4 4-4 1191 1191 1191-1191 571 571 571-571

Last 30 days 4 0.13 24.25 27 4-39 736.50 712 141-1381 11665.75 3064 571-39964

Lifetime (4249 days) 3324 0.78 33.62 24 3-120 572.32 348 7-11276 21112.95 4070 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	4	4	4-4	1191	1191	1191-1191	571	571	571-571
Last 30 days	4	0.13	24.25	27	4-39	736.50	712	141-1381	11665.75	3064	571-39964
Lifetime (4249 days)	3324	0.78	33.62	24	3-120	572.32	348	7-11276	21112.95	4070	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	223	6.7
40-50	250	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	1529	46.0

Number of rate classes	Times found	% found
1	0	0.0
2	2080	62.6
3	729	21.9
4	286	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 Tue Sep 21 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 46 46 46-46 3551 3551 3551-3551 263 263 263-263

Last 30 days 29 0.97 37.07 33 4-87 9589.48 9805 3551-9812 173.48 127 20-472

Lifetime (4128 days) 3722 0.90 36.01 31 3-100 1074.19 556 9-11100 478.32 144 2-31585

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	46	46	46-46	3551	3551	3551-3551	263	263	263-263
Last 30 days	29	0.97	37.07	33	4-87	9589.48	9805	3551-9812	173.48	127	20-472
Lifetime (4128 days)	3722	0.90	36.01	31	3-100	1074.19	556	9-11100	478.32	144	2-31585

Subtyping

SCUEAL usage summary as of Tue Sep 21 00:01:05 2021 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 7163 7163.00 90.08 4 0-500

Last 7 days 7163 1023.29 90.08 4 0-500

Last 30 days 7163 238.77 90.08 4 0-500

Lifetime (4463 days) 8467 1.90 93.43 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	7163	7163.00	90.08	4	0-500
Last 7 days	7163	1023.29	90.08	4	0-500
Last 30 days	7163	238.77	90.08	4	0-500
Lifetime (4463 days)	8467	1.90	93.43	5	0-500

Top 10 Subtypes (out of 791080 sequences)

Subtypes Times found % found

B 312517 39.5

C 152618 19.3

G 51673 6.5

A1 46724 5.9

Complex 33102 4.2

AE 20787 2.6

D 19766 2.5

CRF14 12918 1.6

F1 12543 1.6

B,C recombinant 9836 1.2

Subtypes	Times found	% found
B	312517	39.5
C	152618	19.3
G	51673	6.5
A1	46724	5.9
Complex	33102	4.2
AE	20787	2.6
D	19766	2.5
CRF14	12918	1.6
F1	12543	1.6
B,C recombinant	9836	1.2

Coevolution

BGM usage summary as of Tue Sep 21 00:01:08 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 (3057 days) 8881 2.91 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 (3057 days)	8881	2.91	65.10	30	0-1033	2.25	0.98	0.01-263	2866.47	92	0-2900666

UCSD Viral Evolution Group 2004-2021