Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Thu Mar 4 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 (3756 days) 92479 24.62 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 (3756 days)	92479	24.62	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 Thu Mar 4 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 1 1.00 38 38 38-38 161 161 161-161 397 397 397-397

Last 7 days 30 4.29 33.20 18 7-185 524.30 164.50 154-2694 1058.60 260.50 39-6286

Last 30 days 91 3.03 47.30 19 4-490 610.63 237 35-4401 434.65 69 2-6286

Lifetime (2856 days) 103888 36.38 44.54 24 3-787 488.02 325 1-11276 181.82 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	1	1.00	38	38	38-38	161	161	161-161	397	397	397-397
Last 7 days	30	4.29	33.20	18	7-185	524.30	164.50	154-2694	1058.60	260.50	39-6286
Last 30 days	91	3.03	47.30	19	4-490	610.63	237	35-4401	434.65	69	2-6286
Lifetime (2856 days)	103888	36.38	44.54	24	3-787	488.02	325	1-11276	181.82	46	0-51470

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 47219 45.5
REV 13335 12.8
TRN93 10156 9.8
F81 5435 5.2
010000 3929 3.8
010232 2094 2.0
012012 1582 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 84000 80.9
0.05 0.9 19.1 15363 14.8
0.2 2.1 29.7 2136 2.1
0.25 3.1 31.9 942 0.9
0.01 0.4 14.7 523 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 Thu Mar 4 00:00:30 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 4 0.57 21.50 18 16-34 761 343 154-2204 221.75 155 88-489

Last 30 days 16 0.53 21.62 19.50 4-53 602.38 536 35-2204 120.12 65.50 0-489

Lifetime (2855 days) 58137 20.36 20.71 16 2-110 488.34 323 1-11542 390.02 111 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	4	0.57	21.50	18	16-34	761	343	154-2204	221.75	155	88-489
Last 30 days	16	0.53	21.62	19.50	4-53	602.38	536	35-2204	120.12	65.50	0-489
Lifetime (2855 days)	58137	20.36	20.71	16	2-110	488.34	323	1-11542	390.02	111	0-54132

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 30917 53.2
REV 5702 9.8
F81 3543 6.1
TRN93 3373 5.8
010000 2345 4.0
012012 1223 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 52554 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 Thu Mar 4 00:00:39 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 (3936 days) 1092 0.28 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 (3936 days)	1092	0.28	47.53	37	7-150	568.73	350	16-3789	3765.88	1970.50	31-42841

Model Select.

ModelSelection usage summary as of Thu Mar 4 00:00:41 2021 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 2 2.00 14 14 14-14 486 486 486-486

Last 7 days 36 5.14 14.31 7 3-107 194.64 84 13-2204

Last 30 days 104 3.47 33.15 18 3-490 817.94 180 13-4401

Lifetime (2856 days) 102541 35.90 43.80 22 3-656 523.01 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	2	2.00	14	14	14-14	486	486	486-486
Last 7 days	36	5.14	14.31	7	3-107	194.64	84	13-2204
Last 30 days	104	3.47	33.15	18	3-490	817.94	180	13-4401
Lifetime (2856 days)	102541	35.90	43.80	22	3-656	523.01	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 24628 24.0
TRN93 13100 12.8
F81 8937 8.7
010232 4382 4.3
012012 3590 3.5
012212 3098 3.0
010230 2485 2.4
012232 2435 2.4
012032 2434 2.4
001101 2115 2.1

Model	Times selected	% selected
HKY85	24628	24.0
TRN93	13100	12.8
F81	8937	8.7
010232	4382	4.3
012012	3590	3.5
012212	3098	3.0
010230	2485	2.4
012232	2435	2.4
012032	2434	2.4
001101	2115	2.1

Protein Model Select.

ModelSelectionP usage summary as of Thu Mar 4 00:00:51 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 0

Lifetime (4657 days) 3945 0.85 46.55 25 2-500 674.71 444 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	0
Lifetime (4657 days)	3945	0.85	46.55	25	2-500	674.71	444	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 567 14.4
JTT (Jones,Taylor,Thornton) 410 10.4
BLOSUM62+F 327 8.3
WAG (Whelan and Goldman)+F 325 8.2
HIV (within host)+F 272 6.9
WAG (Whelan and Goldman) 245 6.2
IAV (Influenza A virus)+F 243 6.2
IAV (Influenza A virus) 228 5.8
BLOSUM62 169 4.3
LG (Le and Gascuel) 168 4.3

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)+F	567	14.4
JTT (Jones,Taylor,Thornton)	410	10.4
BLOSUM62+F	327	8.3
WAG (Whelan and Goldman)+F	325	8.2
HIV (within host)+F	272	6.9
WAG (Whelan and Goldman)	245	6.2
IAV (Influenza A virus)+F	243	6.2
IAV (Influenza A virus)	228	5.8
BLOSUM62	169	4.3
LG (Le and Gascuel)	168	4.3

GARD

GARD usage summary as of Thu Mar 4 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 27 3.86 6.07 6 3-9 253.33 240 39-654 140.93 174 49-284

Last 30 days 55 1.83 13.27 7 3-36 2411.65 378 39-12000 907.18 190 49-4339

Lifetime (5209 days) 76077 14.60 26.94 18 2-300 2044.46 1116 20-46625 1292.32 386 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	27	3.86	6.07	6	3-9	253.33	240	39-654	140.93	174	49-284
Last 30 days	55	1.83	13.27	7	3-36	2411.65	378	39-12000	907.18	190	49-4339
Lifetime (5209 days)	76077	14.60	26.94	18	2-300	2044.46	1116	20-46625	1292.32	386	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	64388	84.6
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	27668	36.4
10-20	3031	4.0
20-30	2443	3.2
30-40	2275	3.0
40-50	1870	2.5
50-60	1975	2.6
60-70	1453	1.9
70-80	1325	1.7
80-90	1226	1.6
90-100	1088	1.4
> 100	31723	41.7

Number of breakpoints	Times found	% found
0	23289	30.6
1	19243	25.3
2	12072	15.9
3	7020	9.2
4	4275	5.6
5	2943	3.9
6	1901	2.5
7	1418	1.9
8	940	1.2
9	761	1.0
≥ 10	2215	2.9

SBP

SBP usage summary as of Thu Mar 4 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 1 1.00 7 7 7-7 3 3 3-3 3 3 3-3

Last 7 days 7 1.00 22 18 4-58 64.57 3 1-203 180.29 8 2-923

Last 30 days 21 0.70 83.62 18 3-431 45.19 3 1-258 3454.57 276 2-42886

Lifetime (2856 days) 21231 7.43 50.26 25 2-656 21.75 1 1-45015 606.18 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	1	1.00	7	7	7-7	3	3	3-3	3	3	3-3
Last 7 days	7	1.00	22	18	4-58	64.57	3	1-203	180.29	8	2-923
Last 30 days	21	0.70	83.62	18	3-431	45.19	3	1-258	3454.57	276	2-42886
Lifetime (2856 days)	21231	7.43	50.26	25	2-656	21.75	1	1-45015	606.18	44	0-683633

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	15398	72.5
REV	1315	6.2
010000	565	2.7
F81	503	2.4
TRN93	502	2.4
0123455	287	1.4
010232	215	1.0
012012	137	0.6
0112304567	122	0.6
010230	105	0.5

IC improvement range	Times found	% found
0-10	9190	43.3
10-20	915	4.3
20-30	803	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	7371	34.7

PARRIS

PARRIS usage summary as of Thu Mar 4 00:01:09 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 21.20 18 18-33 696.20 154 154-1538 143 95 80-322

Last 30 days 6 0.20 26.50 18.50 18-53 609 163.50 154-1538 148 115.50 80-322

Lifetime (4964 days) 14597 2.94 20.12 15 3-75 489.66 329 7-11903 425.73 136 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	5	0.71	21.20	18	18-33	696.20	154	154-1538	143	95	80-322
Last 30 days	6	0.20	26.50	18.50	18-53	609	163.50	154-1538	148	115.50	80-322
Lifetime (4964 days)	14597	2.94	20.12	15	3-75	489.66	329	7-11903	425.73	136	1-48648

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8258	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	372	2.5
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	359	2.5
0.8-0.9	355	2.4
0.9-1	8753	60.0

GA Branch

GABranch usage summary as of Thu Mar 4 00:01:11 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 16 16 16-16 2204 2204 2204-2204 9594 9594 9594-9594

Last 30 days 2 0.07 16 16 16-16 1150 1150 96-2204 5302.50 5302.50 1011-9594

Lifetime (4957 days) 11862 2.39 13.74 12 3-30 522.49 333 9-11628 5656.44 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	16	16	16-16	2204	2204	2204-2204	9594	9594	9594-9594
Last 30 days	2	0.07	16	16	16-16	1150	1150	96-2204	5302.50	5302.50	1011-9594
Lifetime (4957 days)	11862	2.39	13.74	12	3-30	522.49	333	9-11628	5656.44	1519	1-889396

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8589	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	36.4
3	4011	33.8
4	2235	18.8
5	780	6.6
6	238	2.0
7	119	1.0
8	39	0.3
9	27	0.2

CMS

CMS usage summary as of Thu Mar 4 00:01:13 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 0

Last 30 days 1 0.03 36 36 36-36 554 554 554-554 24157 24157 24157-24157

Lifetime (4048 days) 3289 0.81 33.72 24 3-120 571.09 345 7-11276 21145.27 4048 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	1	0.03	36	36	36-36	554	554	554-554	24157	24157	24157-24157
Lifetime (4048 days)	3289	0.81	33.72	24	3-120	571.09	345	7-11276	21145.27	4048	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	222	6.7
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	1507	45.8

Number of rate classes	Times found	% found
1	0	0.0
2	2064	62.8
3	720	21.9
4	282	8.6
5	120	3.6
6	51	1.6
7	15	0.5
8	2	0.1
9	1	0.0
≥ 10	34	1.0

DEPS

DEPS usage summary as of Thu Mar 4 00:01:14 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 (3927 days) 3577 0.91 35.84 32 3-100 733.17 528 9-11100 489.42 146 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 (3927 days)	3577	0.91	35.84	32	3-100	733.17	528	9-11100	489.42	146	2-31585

Subtyping

SCUEAL usage summary as of Thu Mar 4 00:01:15 2021 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 7046 7046.00 91.19 4 0-500

Last 7 days 7046 1006.57 91.19 4 0-500

Last 30 days 7046 234.87 91.19 4 0-500

Lifetime (4262 days) 8350 1.96 94.42 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	7046	7046.00	91.19	4	0-500
Last 7 days	7046	1006.57	91.19	4	0-500
Last 30 days	7046	234.87	91.19	4	0-500
Lifetime (4262 days)	8350	1.96	94.42	5	0-500

Top 10 Subtypes (out of 788389 sequences)

Subtypes Times found % found

B 311731 39.5

C 152323 19.3

G 51491 6.5

A1 46605 5.9

Complex 32843 4.2

AE 20769 2.6

D 19699 2.5

CRF14 12916 1.6

F1 12364 1.6

B,C recombinant 9784 1.2

Subtypes	Times found	% found
B	311731	39.5
C	152323	19.3
G	51491	6.5
A1	46605	5.9
Complex	32843	4.2
AE	20769	2.6
D	19699	2.5
CRF14	12916	1.6
F1	12364	1.6
B,C recombinant	9784	1.2

Coevolution

BGM usage summary as of Thu Mar 4 00:01:18 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 (2856 days) 8881 3.11 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 (2856 days)	8881	3.11	65.10	30	0-1033	2.25	0.98	0.01-263	2866.47	92	0-2900666

UCSD Viral Evolution Group 2004-2021