Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Tue Jul 27 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 (3901 days) 92479 23.71 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 (3901 days)	92479	23.71	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 Jul 27 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 8 1.14 85.50 86 35-188 316.62 211 76-985 618.50 430 128-1454

Last 30 days 30 1.00 68.67 38.50 3-258 520.93 507 64-1248 795.20 691.50 82-2225

Lifetime (3001 days) 103997 34.65 44.59 24 3-787 488.09 325 1-11276 182.65 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	8	1.14	85.50	86	35-188	316.62	211	76-985	618.50	430	128-1454
Last 30 days	30	1.00	68.67	38.50	3-258	520.93	507	64-1248	795.20	691.50	82-2225
Lifetime (3001 days)	103997	34.65	44.59	24	3-787	488.09	325	1-11276	182.65	46	0-51470

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 47282 45.5
REV 13370 12.9
TRN93 10158 9.8
F81 5438 5.2
010000 3929 3.8
010232 2094 2.0
012012 1583 1.5
012212 1405 1.4
010230 1270 1.2
012032 1005 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 24.0 84082 80.9
0.05 0.9 19.1 15388 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 5.9 43.2 214 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 Jul 27 00:00:26 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 35 35 35-35 344 344 344-344 162 162 162-162

Last 30 days 44 1.47 25.73 24 3-62 677.27 739 181-920 177.66 168.50 13-484

Lifetime (3000 days) 58285 19.43 20.71 16 2-110 488.35 323 1-11542 389.41 111 0-54132

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	1	0.14	35	35	35-35	344	344	344-344	162	162	162-162
Last 30 days	44	1.47	25.73	24	3-62	677.27	739	181-920	177.66	168.50	13-484
Lifetime (3000 days)	58285	19.43	20.71	16	2-110	488.35	323	1-11542	389.41	111	0-54132

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 31013 53.2
REV 5721 9.8
F81 3547 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 52679 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 Jul 27 00:00:33 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 (4081 days) 1092 0.27 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 (4081 days)	1092	0.27	47.53	37	7-150	568.73	350	16-3789	3765.88	1970.50	31-42841

Model Select.

ModelSelection usage summary as of Tue Jul 27 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 4 0.57 66.25 66 42-91 76.75 76.50 76-78

Last 30 days 49 1.63 33 27 3-109 592.20 739 24-1248

Lifetime (3001 days) 102687 34.22 43.79 22 3-656 523.10 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	4	0.57	66.25	66	42-91	76.75	76.50	76-78
Last 30 days	49	1.63	33	27	3-109	592.20	739	24-1248
Lifetime (3001 days)	102687	34.22	43.79	22	3-656	523.10	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 24656 24.0
TRN93 13107 12.8
F81 8966 8.7
010232 4383 4.3
012012 3612 3.5
012212 3102 3.0
010230 2487 2.4
012032 2439 2.4
012232 2437 2.4
001101 2116 2.1

Model	Times selected	% selected
HKY85	24656	24.0
TRN93	13107	12.8
F81	8966	8.7
010232	4383	4.3
012012	3612	3.5
012212	3102	3.0
010230	2487	2.4
012032	2439	2.4
012232	2437	2.4
001101	2116	2.1

Protein Model Select.

ModelSelectionP usage summary as of Tue Jul 27 00:00:44 2021 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 10 10.00 71.20 88.50 7-92 9768.20 9805 9510-9935

Last 7 days 17 2.43 63.06 88 7-92 9736.71 9805 9510-9935

Last 30 days 29 0.97 73.07 76 7-441 9135.97 9805 111-10018

Lifetime (4802 days) 4001 0.83 46.65 26 2-500 794.34 451 3-18120

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	10	10.00	71.20	88.50	7-92	9768.20	9805	9510-9935
Last 7 days	17	2.43	63.06	88	7-92	9736.71	9805	9510-9935
Last 30 days	29	0.97	73.07	76	7-441	9135.97	9805	111-10018
Lifetime (4802 days)	4001	0.83	46.65	26	2-500	794.34	451	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 567 14.2
JTT (Jones,Taylor,Thornton) 410 10.2
BLOSUM62+F 328 8.2
WAG (Whelan and Goldman)+F 326 8.1
HIV (within host)+F 295 7.4
IAV (Influenza A virus)+F 266 6.6
WAG (Whelan and Goldman) 245 6.1
IAV (Influenza A virus) 228 5.7
BLOSUM62 169 4.2
HIV (between hosts)+F 169 4.2

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)+F	567	14.2
JTT (Jones,Taylor,Thornton)	410	10.2
BLOSUM62+F	328	8.2
WAG (Whelan and Goldman)+F	326	8.1
HIV (within host)+F	295	7.4
IAV (Influenza A virus)+F	266	6.6
WAG (Whelan and Goldman)	245	6.1
IAV (Influenza A virus)	228	5.7
BLOSUM62	169	4.2
HIV (between hosts)+F	169	4.2

GARD

GARD usage summary as of Tue Jul 27 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 5 0.71 98.80 108 42-188 1542.60 1344 228-2955 2022.40 2267 255-3708

Last 30 days 18 0.60 42.83 21.50 3-188 2536.17 2955 72-4896 1677.06 1224.50 34-4041

Lifetime (5354 days) 76200 14.23 26.94 18 2-300 2045.39 1116 20-46625 1292.51 386 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	5	0.71	98.80	108	42-188	1542.60	1344	228-2955	2022.40	2267	255-3708
Last 30 days	18	0.60	42.83	21.50	3-188	2536.17	2955	72-4896	1677.06	1224.50	34-4041
Lifetime (5354 days)	76200	14.23	26.94	18	2-300	2045.39	1116	20-46625	1292.51	386	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	64511	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	27732	36.4
10-20	3031	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	1227	1.6
90-100	1088	1.4
> 100	31774	41.7

Number of breakpoints	Times found	% found
0	23350	30.6
1	19260	25.3
2	12087	15.9
3	7034	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 Jul 27 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 2 0.29 12 12 12-12 1 1 1-1 420 420 381-459

Last 30 days 9 0.30 65.56 12 5-336 28.89 1 1-121 1430.67 381 9-9801

Lifetime (3001 days) 21286 7.09 50.41 25 2-656 21.78 1 1-45015 623.75 44 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	2	0.29	12	12	12-12	1	1	1-1	420	420	381-459
Last 30 days	9	0.30	65.56	12	5-336	28.89	1	1-121	1430.67	381	9-9801
Lifetime (3001 days)	21286	7.09	50.41	25	2-656	21.78	1	1-45015	623.75	44	0-683633

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	15438	72.5
REV	1315	6.2
010000	565	2.7
F81	503	2.4
TRN93	502	2.4
0123455	293	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	9206	43.2
10-20	916	4.3
20-30	805	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	293	1.4
90-100	329	1.5
> 100	7403	34.8

PARRIS

PARRIS usage summary as of Tue Jul 27 00:01:00 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 (5109 days) 14607 2.86 20.12 15 3-75 489.63 329 7-11903 425.56 136 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	0
Lifetime (5109 days)	14607	2.86	20.12	15	3-75	489.63	329	7-11903	425.56	136	1-48648

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8268	56.6
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	2668	18.3
0.1-0.2	518	3.5
0.2-0.3	476	3.3
0.3-0.4	373	2.6
0.4-0.5	331	2.3
0.5-0.6	393	2.7
0.6-0.7	373	2.6
0.7-0.8	360	2.5
0.8-0.9	355	2.4
0.9-1	8760	60.0

GA Branch

GABranch usage summary as of Tue Jul 27 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 0

Lifetime (5102 days) 11882 2.33 13.75 12 3-30 522.52 333 9-11628 5654.04 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	0
Lifetime (5102 days)	11882	2.33	13.75	12	3-30	522.52	333	9-11628	5654.04	1519	1-889396

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8609	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	4315	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 Jul 27 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 13 13 13-13 1834 1834 1834-1834 6278 6278 6278-6278

Last 30 days 5 0.17 20.20 22 9-33 671.20 544 156-1834 6587.60 6278 445-17622

Lifetime (4193 days) 3316 0.79 33.64 24 3-120 572.33 348 7-11276 21139.47 4060 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	13	13	13-13	1834	1834	1834-1834	6278	6278	6278-6278
Last 30 days	5	0.17	20.20	22	9-33	671.20	544	156-1834	6587.60	6278	445-17622
Lifetime (4193 days)	3316	0.79	33.64	24	3-120	572.33	348	7-11276	21139.47	4060	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	5.9
30-40	223	6.7
40-50	249	7.5
50-60	184	5.5
60-70	178	5.4
70-80	129	3.9
80-90	178	5.4
90-100	111	3.3
> 100	1525	46.0

Number of rate classes	Times found	% found
1	0	0.0
2	2075	62.6
3	728	22.0
4	284	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 Jul 27 00:01:05 2021 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 13 13.00 75.31 89 7-92 9776.69 9805 9510-9935 391.08 454 33-540

Last 7 days 19 2.71 65.79 88 7-92 9743.89 9805 9510-9935 321.58 374 24-540

Last 30 days 27 0.90 57.85 81 7-92 9797.04 9805 9510-10018 301.33 319 24-1113

Lifetime (4072 days) 3642 0.89 35.92 31 3-100 890.96 540 9-11100 484.12 144 2-31585

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	13	13.00	75.31	89	7-92	9776.69	9805	9510-9935	391.08	454	33-540
Last 7 days	19	2.71	65.79	88	7-92	9743.89	9805	9510-9935	321.58	374	24-540
Last 30 days	27	0.90	57.85	81	7-92	9797.04	9805	9510-10018	301.33	319	24-1113
Lifetime (4072 days)	3642	0.89	35.92	31	3-100	890.96	540	9-11100	484.12	144	2-31585

Subtyping

SCUEAL usage summary as of Tue Jul 27 00:01:07 2021 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 7122 7122.00 90.54 4 0-500

Last 7 days 7122 1017.43 90.54 4 0-500

Last 30 days 7122 237.40 90.54 4 0-500

Lifetime (4407 days) 8426 1.91 93.84 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	7122	7122.00	90.54	4	0-500
Last 7 days	7122	1017.43	90.54	4	0-500
Last 30 days	7122	237.40	90.54	4	0-500
Lifetime (4407 days)	8426	1.91	93.84	5	0-500

Top 10 Subtypes (out of 790686 sequences)

Subtypes Times found % found

B 312432 39.5

C 152608 19.3

G 51613 6.5

A1 46710 5.9

Complex 33039 4.2

AE 20785 2.6

D 19758 2.5

CRF14 12918 1.6

F1 12537 1.6

B,C recombinant 9834 1.2

Subtypes	Times found	% found
B	312432	39.5
C	152608	19.3
G	51613	6.5
A1	46710	5.9
Complex	33039	4.2
AE	20785	2.6
D	19758	2.5
CRF14	12918	1.6
F1	12537	1.6
B,C recombinant	9834	1.2

Coevolution

BGM usage summary as of Tue Jul 27 00:01:10 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 (3001 days) 8881 2.96 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 (3001 days)	8881	2.96	65.10	30	0-1033	2.25	0.98	0.01-263	2866.47	92	0-2900666

UCSD Viral Evolution Group 2004-2021