Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Sun Dec 8 00:00:01 2019 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 (3304 days) 92479 27.99 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 (3304 days)	92479	27.99	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 Dec 8 00:00:13 2019 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 59.41 48 3-251 201.41 80 76-973 692.59 370 242-4157

Last 30 days 80 2.67 51.42 30 3-327 575.60 325 76-3443 2070.03 924.50 190-14824

Lifetime (2404 days) 102396 42.59 44.32 24 3-787 484.14 325 1-11276 156.62 45 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	17	2.43	59.41	48	3-251	201.41	80	76-973	692.59	370	242-4157
Last 30 days	80	2.67	51.42	30	3-327	575.60	325	76-3443	2070.03	924.50	190-14824
Lifetime (2404 days)	102396	42.59	44.32	24	3-787	484.14	325	1-11276	156.62	45	0-51470

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 46335 45.3
REV 13224 12.9
TRN93 10067 9.8
F81 5269 5.1
010000 3926 3.8
010232 2082 2.0
012012 1581 1.5
012212 1386 1.4
010230 1254 1.2
012032 996 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 24.1 82813 80.9
0.05 0.9 19.1 15141 14.8
0.2 2.1 29.8 2118 2.1
0.25 3.1 32.5 909 0.9
0.01 0.4 14.7 520 0.5
0.5 5.9 43.2 214 0.2
0.15 2.5 23.5 161 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 Dec 8 00:00:27 2019 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 6 6 6-6 89 89 89-89 124 124 124-124

Last 7 days 39 5.57 16.49 10 3-74 229.08 89 45-909 185.56 123 23-962

Last 30 days 54 1.80 18.89 15 3-74 279.09 169.50 45-909 512.35 134.50 23-4566

Lifetime (2403 days) 57060 23.75 20.68 16 2-110 485.22 323 1-10798 389.14 110 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	6	6	6-6	89	89	89-89	124	124	124-124
Last 7 days	39	5.57	16.49	10	3-74	229.08	89	45-909	185.56	123	23-962
Last 30 days	54	1.80	18.89	15	3-74	279.09	169.50	45-909	512.35	134.50	23-4566
Lifetime (2403 days)	57060	23.75	20.68	16	2-110	485.22	323	1-10798	389.14	110	0-54132

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 30271 53.1
REV 5668 9.9
F81 3386 5.9
TRN93 3336 5.8
010000 2339 4.1
012012 1202 2.1
001101 728 1.3
012212 704 1.2
010232 694 1.2
012032 614 1.1

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

50 4.3 27.9 51622 90.5
100 4.3 22.4 1301 2.3
90 19.2 11.2 900 1.6
20 7.2 35.9 820 1.4
10 5.8 31.9 747 1.3
95 2.2 30.9 715 1.3
40 2.5 24.4 145 0.3
80 3.0 28.0 109 0.2
30 10.0 20.2 91 0.2
25 3.4 36.7 86 0.2

TOGGLE

Toggle usage summary as of Sun Dec 8 00:00:33 2019 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 22 22 22-22 1032 1032 1032-1032 483 483 483-483

Lifetime (3484 days) 1080 0.31 47.61 37 7-150 571.65 350 16-3789 3784.18 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	1	0.03	22	22	22-22	1032	1032	1032-1032	483	483	483-483
Lifetime (3484 days)	1080	0.31	47.61	37	7-150	571.65	350	16-3789	3784.18	1970.50	31-42841

Model Select.

ModelSelection usage summary as of Sun Dec 8 00:00:35 2019 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 2 2.00 86.50 86.50 6-167 496.50 496.50 89-904

Last 7 days 26 3.71 23.58 11 3-167 256.58 89 45-1053

Last 30 days 131 4.37 29.48 17 3-167 450.37 351 45-3434

Lifetime (2404 days) 100904 41.97 43.67 22 3-656 519.95 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	2	2.00	86.50	86.50	6-167	496.50	496.50	89-904
Last 7 days	26	3.71	23.58	11	3-167	256.58	89	45-1053
Last 30 days	131	4.37	29.48	17	3-167	450.37	351	45-3434
Lifetime (2404 days)	100904	41.97	43.67	22	3-656	519.95	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 24237 24.0
TRN93 12995 12.9
F81 8689 8.6
010232 4314 4.3
012012 3529 3.5
012212 3044 3.0
010230 2457 2.4
012032 2401 2.4
012232 2400 2.4
001101 2096 2.1

Model	Times selected	% selected
HKY85	24237	24.0
TRN93	12995	12.9
F81	8689	8.6
010232	4314	4.3
012012	3529	3.5
012212	3044	3.0
010230	2457	2.4
012032	2401	2.4
012232	2400	2.4
001101	2096	2.1

Protein Model Select.

ModelSelectionP usage summary as of Sun Dec 8 00:00:44 2019 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 (4205 days) 3879 0.92 46.47 25 2-500 652.08 444 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 (4205 days)	3879	0.92	46.47	25	2-500	652.08	444	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 562 14.5
JTT (Jones,Taylor,Thornton) 406 10.5
BLOSUM62+F 326 8.4
WAG (Whelan and Goldman)+F 321 8.3
HIV (within host)+F 253 6.5
WAG (Whelan and Goldman) 244 6.3
IAV (Influenza A virus)+F 241 6.2
IAV (Influenza A virus) 225 5.8
BLOSUM62 168 4.3
LG (Le and Gascuel) 162 4.2

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)+F	562	14.5
JTT (Jones,Taylor,Thornton)	406	10.5
BLOSUM62+F	326	8.4
WAG (Whelan and Goldman)+F	321	8.3
HIV (within host)+F	253	6.5
WAG (Whelan and Goldman)	244	6.3
IAV (Influenza A virus)+F	241	6.2
IAV (Influenza A virus)	225	5.8
BLOSUM62	168	4.3
LG (Le and Gascuel)	162	4.2

GARD

GARD usage summary as of Sun Dec 8 00:00:46 2019 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 4 4.00 28 28 28-28 2338 2338 2338-2338 3535.75 3626 3264-3627

Last 7 days 7 1.00 30.43 28 8-49 1452.14 2338 228-2338 2237.57 3264 314-3627

Last 30 days 37 1.23 42.35 39 7-143 3937.68 1683 228-10341 1929.57 1623 122-5934

Lifetime (4757 days) 75313 15.83 26.87 18 2-300 2036.84 1116 20-46625 1288.74 383 1-272974

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	4	4.00	28	28	28-28	2338	2338	2338-2338	3535.75	3626	3264-3627
Last 7 days	7	1.00	30.43	28	8-49	1452.14	2338	228-2338	2237.57	3264	314-3627
Last 30 days	37	1.23	42.35	39	7-143	3937.68	1683	228-10341	1929.57	1623	122-5934
Lifetime (4757 days)	75313	15.83	26.87	18	2-300	2036.84	1116	20-46625	1288.74	383	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	63624	84.5
HKY85	5991	8.0
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	27346	36.3
10-20	2999	4.0
20-30	2428	3.2
30-40	2259	3.0
40-50	1854	2.5
50-60	1961	2.6
60-70	1436	1.9
70-80	1316	1.7
80-90	1219	1.6
90-100	1083	1.4
> 100	31412	41.7

Number of breakpoints	Times found	% found
0	23006	30.5
1	19055	25.3
2	11948	15.9
3	6948	9.2
4	4240	5.6
5	2910	3.9
6	1882	2.5
7	1413	1.9
8	935	1.2
9	761	1.0
≥ 10	2215	2.9

SBP

SBP usage summary as of Sun Dec 8 00:00:56 2019 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 6 6.00 26.50 28 19-28 1 1 1-1 525.67 607.50 85-636

Last 7 days 6 0.86 26.50 28 19-28 1 1 1-1 525.67 607.50 85-636

Last 30 days 47 1.57 23.06 15 3-197 12.47 1 1-369 255.36 187 2-1718

Lifetime (2404 days) 20850 8.67 49.81 25 2-656 21.77 1 1-45015 597.11 42 0-683633

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	6	6.00	26.50	28	19-28	1	1	1-1	525.67	607.50	85-636
Last 7 days	6	0.86	26.50	28	19-28	1	1	1-1	525.67	607.50	85-636
Last 30 days	47	1.57	23.06	15	3-197	12.47	1	1-369	255.36	187	2-1718
Lifetime (2404 days)	20850	8.67	49.81	25	2-656	21.77	1	1-45015	597.11	42	0-683633

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	15094	72.4
REV	1315	6.3
010000	565	2.7
F81	503	2.4
TRN93	502	2.4
0123455	246	1.2
010232	215	1.0
012012	137	0.7
0112304567	119	0.6
010230	105	0.5

IC improvement range	Times found	% found
0-10	9030	43.3
10-20	899	4.3
20-30	796	3.8
30-40	648	3.1
40-50	511	2.5
50-60	410	2.0
60-70	359	1.7
70-80	376	1.8
80-90	285	1.4
90-100	319	1.5
> 100	7217	34.6

PARRIS

PARRIS usage summary as of Sun Dec 8 00:00:59 2019 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 3 0.43 20 20 20-20 921 921 921-921 91.33 92 89-93

Last 30 days 14 0.47 20.93 21.50 16-24 966.86 958 829-1079 217.93 189 89-494

Lifetime (4512 days) 14443 3.20 20.13 15 3-75 486.47 329 7-11903 426.55 137 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	3	0.43	20	20	20-20	921	921	921-921	91.33	92	89-93
Last 30 days	14	0.47	20.93	21.50	16-24	966.86	958	829-1079	217.93	189	89-494
Lifetime (4512 days)	14443	3.20	20.13	15	3-75	486.47	329	7-11903	426.55	137	1-48648

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8174	56.6
F81	1068	7.4
REV	1008	7.0
TRN93	758	5.2
010000	429	3.0
012012	259	1.8
001101	166	1.1
012212	155	1.1
012032	132	0.9
010230	125	0.9

p-values range	Times found	% found
0-0.1	2634	18.2
0.1-0.2	514	3.6
0.2-0.3	465	3.2
0.3-0.4	366	2.5
0.4-0.5	331	2.3
0.5-0.6	391	2.7
0.6-0.7	370	2.6
0.7-0.8	358	2.5
0.8-0.9	354	2.5
0.9-1	8660	60.0

GA Branch

GABranch usage summary as of Sun Dec 8 00:01:01 2019 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 19 19 19-19 1053 1053 1053-1053 19814 19814 19814-19814

Last 30 days 1 0.03 19 19 19-19 1053 1053 1053-1053 19814 19814 19814-19814

Lifetime (4505 days) 11730 2.60 13.73 12 3-30 520.00 332 9-11628 5664.29 1521 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	19	19	19-19	1053	1053	1053-1053	19814	19814	19814-19814
Last 30 days	1	0.03	19	19	19-19	1053	1053	1053-1053	19814	19814	19814-19814
Lifetime (4505 days)	11730	2.60	13.73	12	3-30	520.00	332	9-11628	5664.29	1521	1-889396

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8457	72.1
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	4285	36.5
3	3958	33.7
4	2199	18.7
5	774	6.6
6	234	2.0
7	118	1.0
8	38	0.3
9	25	0.2

CMS

CMS usage summary as of Sun Dec 8 00:01:03 2019 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 17 17 8-26 117 117 116-118 1079.50 1079.50 910-1249

Last 30 days 2 0.07 17 17 8-26 117 117 116-118 1079.50 1079.50 910-1249

Lifetime (3596 days) 3208 0.89 33.70 24 3-120 563.64 340 7-11276 21203.02 4066.50 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	2	0.29	17	17	8-26	117	117	116-118	1079.50	1079.50	910-1249
Last 30 days	2	0.07	17	17	8-26	117	117	116-118	1079.50	1079.50	910-1249
Lifetime (3596 days)	3208	0.89	33.70	24	3-120	563.64	340	7-11276	21203.02	4066.50	59-3262277

Distribution of mBIC improvement

Number of inferred rate classes

mBIC improvement range	Times found	% found
0-10	184	5.7
10-20	147	4.6
20-30	189	5.9
30-40	217	6.8
40-50	243	7.6
50-60	179	5.6
60-70	174	5.4
70-80	129	4.0
80-90	175	5.5
90-100	108	3.4
> 100	1463	45.6

Number of rate classes	Times found	% found
1	0	0.0
2	2017	62.9
3	707	22.0
4	272	8.5
5	112	3.5
6	48	1.5
7	15	0.5
8	2	0.1
9	1	0.0
≥ 10	34	1.1

DEPS

DEPS usage summary as of Sun Dec 8 00:01:04 2019 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 80 80 80-80 161 161 161-161 587 587 587-587

Last 30 days 1 0.03 80 80 80-80 161 161 161-161 587 587 587-587

Lifetime (3475 days) 3407 0.98 35.24 30 3-100 653.05 501 9-11100 500.89 140 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	80	80	80-80	161	161	161-161	587	587	587-587
Last 30 days	1	0.03	80	80	80-80	161	161	161-161	587	587	587-587
Lifetime (3475 days)	3407	0.98	35.24	30	3-100	653.05	501	9-11100	500.89	140	2-31585

Subtyping

SCUEAL usage summary as of Sun Dec 8 00:01:06 2019 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 6436 6436.00 81.59 3 0-500

Last 7 days 6436 919.43 81.59 3 0-500

Last 30 days 6436 214.53 81.59 3 0-500

Lifetime (3810 days) 7740 2.03 86.69 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	6436	6436.00	81.59	3	0-500
Last 7 days	6436	919.43	81.59	3	0-500
Last 30 days	6436	214.53	81.59	3	0-500
Lifetime (3810 days)	7740	2.03	86.69	5	0-500

Top 10 Subtypes (out of 670946 sequences)

Subtypes Times found % found

B 261162 38.9

C 117176 17.5

G 46069 6.9

A1 42088 6.3

Complex 28207 4.2

AE 19814 3.0

D 18959 2.8

CRF14 11763 1.8

F1 10613 1.6

B,C recombinant 9164 1.4

Subtypes	Times found	% found
B	261162	38.9
C	117176	17.5
G	46069	6.9
A1	42088	6.3
Complex	28207	4.2
AE	19814	3.0
D	18959	2.8
CRF14	11763	1.8
F1	10613	1.6
B,C recombinant	9164	1.4

Coevolution

BGM usage summary as of Sun Dec 8 00:01:08 2019 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 (2404 days) 8881 3.69 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 (2404 days)	8881	3.69	65.10	30	0-1033	2.25	0.98	0.01-263	2866.47	92	0-2900666

UCSD Viral Evolution Group 2004-2019