Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Sun May 16 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 (3829 days) 92479 24.15 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 (3829 days)	92479	24.15	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 Sun May 16 00:00:20 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 16 0.53 39.31 25.50 6-168 603.88 638 150-1175 87.94 53.50 8-353

Lifetime (2929 days) 103965 35.50 44.59 24 3-787 488.08 325 1-11276 182.47 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	0
Last 30 days	16	0.53	39.31	25.50	6-168	603.88	638	150-1175	87.94	53.50	8-353
Lifetime (2929 days)	103965	35.50	44.59	24	3-787	488.08	325	1-11276	182.47	46	0-51470

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 47265 45.5
REV 13359 12.8
TRN93 10156 9.8
F81 5437 5.2
010000 3929 3.8
010232 2094 2.0
012012 1583 1.5
012212 1405 1.4
010230 1269 1.2
012032 1005 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 24.0 84061 80.9
0.05 0.9 19.1 15377 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 Sun May 16 00:00:42 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 5 0.17 33.80 40 18-42 358 398 243-488 110.40 133 12-165

Lifetime (2928 days) 58173 19.87 20.71 16 2-110 488.34 323 1-11542 389.97 111 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	0
Last 30 days	5	0.17	33.80	40	18-42	358	398	243-488	110.40	133	12-165
Lifetime (2928 days)	58173	19.87	20.71	16	2-110	488.34	323	1-11542	389.97	111	0-54132

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 30952 53.2
REV 5702 9.8
F81 3543 6.1
TRN93 3373 5.8
010000 2345 4.0
012012 1224 2.1
001101 730 1.3
012212 718 1.2
010232 709 1.2
012032 619 1.1

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

50 4.3 27.8 52590 90.4
100 4.4 22.1 1318 2.3
90 19.2 11.2 901 1.5
20 7.2 36.0 826 1.4
95 2.4 31.6 767 1.3
10 5.8 31.9 747 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 Sun May 16 00:00:53 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 (4009 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 (4009 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 Sun May 16 00:01:00 2021 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 0

Last 30 days 6 0.20 58.83 29.50 6-234 463.28 274 177- 1376.67

Lifetime (2929 days) 102637 35.04 43.80 22 3-656 523.06 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	0
Last 30 days	6	0.20	58.83	29.50	6-234	463.28	274	177- 1376.67
Lifetime (2929 days)	102637	35.04	43.80	22	3-656	523.06	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 24648 24.0
TRN93 13104 12.8
F81 8961 8.7
010232 4383 4.3
012012 3595 3.5
012212 3098 3.0
010230 2486 2.4
012232 2436 2.4
012032 2435 2.4
001101 2116 2.1

Model	Times selected	% selected
HKY85	24648	24.0
TRN93	13104	12.8
F81	8961	8.7
010232	4383	4.3
012012	3595	3.5
012212	3098	3.0
010230	2486	2.4
012232	2436	2.4
012032	2435	2.4
001101	2116	2.1

Protein Model Select.

ModelSelectionP usage summary as of Sun May 16 00:01:17 2021 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 0

Last 30 days 2 0.07 24 24 24-24 9927 9927 9927-9927

Lifetime (4730 days) 3972 0.84 46.45 25 2-500 733.43 448 3-18120

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	0
Last 30 days	2	0.07	24	24	24-24	9927	9927	9927-9927
Lifetime (4730 days)	3972	0.84	46.45	25	2-500	733.43	448	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 567 14.3
JTT (Jones,Taylor,Thornton) 410 10.3
BLOSUM62+F 327 8.2
WAG (Whelan and Goldman)+F 326 8.2
HIV (within host)+F 284 7.2
IAV (Influenza A virus)+F 256 6.4
WAG (Whelan and Goldman) 245 6.2
IAV (Influenza A virus) 228 5.7
BLOSUM62 169 4.3
LG (Le and Gascuel) 168 4.2

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)+F	567	14.3
JTT (Jones,Taylor,Thornton)	410	10.3
BLOSUM62+F	327	8.2
WAG (Whelan and Goldman)+F	326	8.2
HIV (within host)+F	284	7.2
IAV (Influenza A virus)+F	256	6.4
WAG (Whelan and Goldman)	245	6.2
IAV (Influenza A virus)	228	5.7
BLOSUM62	169	4.3
LG (Le and Gascuel)	168	4.2

GARD

GARD usage summary as of Sun May 16 00:01:19 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 6 0.20 19.67 16.50 6-45 1480.17 965.50 822-4130 1298 363.50 103-3672

Lifetime (5282 days) 76154 14.42 26.93 18 2-300 2044.60 1116 20-46625 1292.02 386 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	0
Last 30 days	6	0.20	19.67	16.50	6-45	1480.17	965.50	822-4130	1298	363.50	103-3672
Lifetime (5282 days)	76154	14.42	26.93	18	2-300	2044.60	1116	20-46625	1292.02	386	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	64465	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	27716	36.4
10-20	3031	4.0
20-30	2445	3.2
30-40	2276	3.0
40-50	1871	2.5
50-60	1976	2.6
60-70	1453	1.9
70-80	1325	1.7
80-90	1227	1.6
90-100	1088	1.4
> 100	31746	41.7

Number of breakpoints	Times found	% found
0	23334	30.6
1	19254	25.3
2	12081	15.9
3	7024	9.2
4	4278	5.6
5	2946	3.9
6	1901	2.5
7	1419	1.9
8	940	1.2
9	762	1.0
≥ 10	2215	2.9

SBP

SBP usage summary as of Sun May 16 00:01:35 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 6 0.20 19.83 20 6-40 123.33 1 1-368 342.83 110.50 0-922

Lifetime (2929 days) 21244 7.25 50.26 25 2-656 21.77 1 1-45015 606.19 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	0
Last 30 days	6	0.20	19.83	20	6-40	123.33	1	1-368	342.83	110.50	0-922
Lifetime (2929 days)	21244	7.25	50.26	25	2-656	21.77	1	1-45015	606.19	44	0-683633

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	15406	72.5
REV	1315	6.2
010000	565	2.7
F81	503	2.4
TRN93	502	2.4
0123455	288	1.4
010232	215	1.0
012012	137	0.6
0112304567	124	0.6
010230	105	0.5

IC improvement range	Times found	% found
0-10	9194	43.3
10-20	915	4.3
20-30	804	3.8
30-40	658	3.1
40-50	520	2.4
50-60	413	1.9
60-70	361	1.7
70-80	378	1.8
80-90	293	1.4
90-100	329	1.5
> 100	7379	34.7

PARRIS

PARRIS usage summary as of Sun May 16 00:01:41 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 18 18 18-18 243 243 243-243 23 23 23-23

Lifetime (5037 days) 14599 2.90 20.11 15 3-75 489.65 329 7-11903 425.68 136 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	18	18	18-18	243	243	243-243	23	23	23-23
Lifetime (5037 days)	14599	2.90	20.11	15	3-75	489.65	329	7-11903	425.68	136	1-48648

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8260	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	475	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	8753	60.0

GA Branch

GABranch usage summary as of Sun May 16 00:01:46 2021 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 1 1.00 26 26 26-26 784 784 784-784 38380 38380 38380-38380

Last 7 days 2 0.29 26 26 26-26 784 784 784-784 29748.50 29748.50 21117-38380

Last 30 days 12 0.40 15.83 11.50 6-27 583.67 567 449-784 5813.08 372.50 137-38380

Lifetime (5030 days) 11878 2.36 13.75 12 3-30 522.53 333 9-11628 5655.52 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	1	1.00	26	26	26-26	784	784	784-784	38380	38380	38380-38380
Last 7 days	2	0.29	26	26	26-26	784	784	784-784	29748.50	29748.50	21117-38380
Last 30 days	12	0.40	15.83	11.50	6-27	583.67	567	449-784	5813.08	372.50	137-38380
Lifetime (5030 days)	11878	2.36	13.75	12	3-30	522.53	333	9-11628	5655.52	1519	1-889396

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8605	72.4
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	4314	36.3
3	4021	33.9
4	2239	18.8
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 Sun May 16 00:01:52 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 2 0.07 25 25 18-32 591.50 591.50 227-956 2978 2978 1741-4215

Lifetime (4121 days) 3295 0.80 33.69 24 3-120 571.88 346 7-11276 21130.81 4066 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	0
Last 30 days	2	0.07	25	25	18-32	591.50	591.50	227-956	2978	2978	1741-4215
Lifetime (4121 days)	3295	0.80	33.69	24	3-120	571.88	346	7-11276	21130.81	4066	59-3262277

Distribution of mBIC improvement

Number of inferred rate classes

mBIC improvement range	Times found	% found
0-10	192	5.8
10-20	151	4.6
20-30	193	5.9
30-40	223	6.8
40-50	249	7.6
50-60	180	5.5
60-70	177	5.4
70-80	129	3.9
80-90	178	5.4
90-100	111	3.4
> 100	1512	45.9

Number of rate classes	Times found	% found
1	0	0.0
2	2065	62.7
3	722	21.9
4	283	8.6
5	121	3.7
6	52	1.6
7	15	0.5
8	2	0.1
9	1	0.0
≥ 10	34	1.0

DEPS

DEPS usage summary as of Sun May 16 00:01:54 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 (4000 days) 3614 0.90 35.76 31 3-100 824.61 536.50 9-11100 485.61 144 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	0
Last 30 days	0
Lifetime (4000 days)	3614	0.90	35.76	31	3-100	824.61	536.50	9-11100	485.61	144	2-31585

Subtyping

SCUEAL usage summary as of Sun May 16 00:01:57 2021 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 7081 7081.00 90.80 4 0-500

Last 7 days 7081 1011.57 90.80 4 0-500

Last 30 days 7081 236.03 90.80 4 0-500

Lifetime (4335 days) 8385 1.93 94.07 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	7081	7081.00	90.80	4	0-500
Last 7 days	7081	1011.57	90.80	4	0-500
Last 30 days	7081	236.03	90.80	4	0-500
Lifetime (4335 days)	8385	1.93	94.07	5	0-500

Top 10 Subtypes (out of 788778 sequences)

Subtypes Times found % found

B 311874 39.5

C 152357 19.3

G 51493 6.5

A1 46609 5.9

Complex 32866 4.2

AE 20778 2.6

D 19700 2.5

CRF14 12916 1.6

F1 12367 1.6

B,C recombinant 9827 1.2

Subtypes	Times found	% found
B	311874	39.5
C	152357	19.3
G	51493	6.5
A1	46609	5.9
Complex	32866	4.2
AE	20778	2.6
D	19700	2.5
CRF14	12916	1.6
F1	12367	1.6
B,C recombinant	9827	1.2

Coevolution

BGM usage summary as of Sun May 16 00:02:01 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 (2929 days) 8881 3.03 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 (2929 days)	8881	3.03	65.10	30	0-1033	2.25	0.98	0.01-263	2866.47	92	0-2900666

UCSD Viral Evolution Group 2004-2021