Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Tue Oct 22 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 (3257 days) 92479 28.39 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 (3257 days)	92479	28.39	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 Oct 22 00:00:34 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 92.50 85 60-140 233.75 178 75-504 110.75 83 17-260

Last 7 days 23 3.29 49.83 48 3-140 462.52 449 75-2123 167.74 96 16-609

Last 30 days 123 4.10 46.76 32 3-499 600.24 325 32-3958 448.59 67 2-18955

Lifetime (2357 days) 102269 43.39 44.31 24 3-787 484.08 325 1-11276 155.04 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	4	4.00	92.50	85	60-140	233.75	178	75-504	110.75	83	17-260
Last 7 days	23	3.29	49.83	48	3-140	462.52	449	75-2123	167.74	96	16-609
Last 30 days	123	4.10	46.76	32	3-499	600.24	325	32-3958	448.59	67	2-18955
Lifetime (2357 days)	102269	43.39	44.31	24	3-787	484.08	325	1-11276	155.04	45	0-51470

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 46251 45.2
REV 13220 12.9
TRN93 10052 9.8
F81 5261 5.1
010000 3926 3.8
010232 2082 2.0
012012 1581 1.5
012212 1386 1.4
010230 1244 1.2
012032 996 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 24.1 82693 80.9
0.05 0.9 19.1 15136 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 Tue Oct 22 00:00:57 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 12 1.71 18.67 17 9-30 500.58 303 238-2123 803.25 104 15-5867

Last 30 days 94 3.13 28.95 31 3-69 748.56 480.50 113-3957 1060.95 198 0-39638

Lifetime (2356 days) 56983 24.19 20.68 16 2-110 485.46 323 1-10798 389.14 111 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	12	1.71	18.67	17	9-30	500.58	303	238-2123	803.25	104	15-5867
Last 30 days	94	3.13	28.95	31	3-69	748.56	480.50	113-3957	1060.95	198	0-39638
Lifetime (2356 days)	56983	24.19	20.68	16	2-110	485.46	323	1-10798	389.14	111	0-54132

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 30213 53.0
REV 5666 9.9
F81 3374 5.9
TRN93 3336 5.9
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 51546 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 30.8 714 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 Tue Oct 22 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 0

Last 30 days 1 0.03 57 57 57-57 293 293 293-293 10278 10278 10278-10278

Lifetime (3437 days) 1079 0.31 47.63 37 7-150 571.23 350 16-3789 3787.24 1973 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	57	57	57-57	293	293	293-293	10278	10278	10278-10278
Lifetime (3437 days)	1079	0.31	47.63	37	7-150	571.23	350	16-3789	3787.24	1973	31-42841

Model Select.

ModelSelection usage summary as of Tue Oct 22 00:01:06 2019 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 5 5.00 99 104 60-140 257.40 226 75-504

Last 7 days 20 2.86 78.05 73.50 13-140 409.70 314.50 75-2123

Last 30 days 196 6.53 39.42 25 3-289 751.27 807 32-3958

Lifetime (2357 days) 100725 42.73 43.68 22 3-656 520.03 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	5	5.00	99	104	60-140	257.40	226	75-504
Last 7 days	20	2.86	78.05	73.50	13-140	409.70	314.50	75-2123
Last 30 days	196	6.53	39.42	25	3-289	751.27	807	32-3958
Lifetime (2357 days)	100725	42.73	43.68	22	3-656	520.03	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 24153 24.0
TRN93 12979 12.9
F81 8672 8.6
010232 4314 4.3
012012 3526 3.5
012212 3043 3.0
010230 2447 2.4
012032 2399 2.4
012232 2398 2.4
001101 2096 2.1

Model	Times selected	% selected
HKY85	24153	24.0
TRN93	12979	12.9
F81	8672	8.6
010232	4314	4.3
012012	3526	3.5
012212	3043	3.0
010230	2447	2.4
012032	2399	2.4
012232	2398	2.4
001101	2096	2.1

Protein Model Select.

ModelSelectionP usage summary as of Tue Oct 22 00:01:15 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 2 0.07 53.50 53.50 11-96 1927 1927 318-3536

Lifetime (4158 days) 3879 0.93 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	2	0.07	53.50	53.50	11-96	1927	1927	318-3536
Lifetime (4158 days)	3879	0.93	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 Tue Oct 22 00:01:17 2019 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 3 3.00 103.33 104 66-140 860 678 390-1512 744.33 640 227-1366

Last 7 days 15 2.14 61.60 57 11-143 1432.27 909 279-6369 1313.13 736 227-4357

Last 30 days 99 3.30 24.30 16 3-143 2377.60 2529 171-11871 2229.59 1147 147-72780

Lifetime (4710 days) 75236 15.97 26.86 18 2-300 2036.16 1116 20-46625 1288.54 383 1-272974

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	3	3.00	103.33	104	66-140	860	678	390-1512	744.33	640	227-1366
Last 7 days	15	2.14	61.60	57	11-143	1432.27	909	279-6369	1313.13	736	227-4357
Last 30 days	99	3.30	24.30	16	3-143	2377.60	2529	171-11871	2229.59	1147	147-72780
Lifetime (4710 days)	75236	15.97	26.86	18	2-300	2036.16	1116	20-46625	1288.54	383	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	63547	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	27312	36.3
10-20	2998	4.0
20-30	2425	3.2
30-40	2258	3.0
40-50	1853	2.5
50-60	1956	2.6
60-70	1432	1.9
70-80	1316	1.7
80-90	1219	1.6
90-100	1082	1.4
> 100	31385	41.7

Number of breakpoints	Times found	% found
0	22974	30.5
1	19032	25.3
2	11937	15.9
3	6944	9.2
4	4237	5.6
5	2909	3.9
6	1879	2.5
7	1413	1.9
8	935	1.2
9	761	1.0
≥ 10	2215	2.9

SBP

SBP usage summary as of Tue Oct 22 00:01:26 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 9 1.29 23.44 24 3-53 1.67 1 1-3 656.11 234 8-1983

Last 30 days 18 0.60 67.17 39.50 3-274 2.22 1 1-11 3229.39 263 8-36189

Lifetime (2357 days) 20785 8.82 49.86 25 2-656 21.80 1 1-45015 598.05 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	0
Last 7 days	9	1.29	23.44	24	3-53	1.67	1	1-3	656.11	234	8-1983
Last 30 days	18	0.60	67.17	39.50	3-274	2.22	1	1-11	3229.39	263	8-36189
Lifetime (2357 days)	20785	8.82	49.86	25	2-656	21.80	1	1-45015	598.05	42	0-683633

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	15031	72.3
REV	1315	6.3
010000	565	2.7
F81	503	2.4
TRN93	502	2.4
0123455	244	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	9012	43.4
10-20	899	4.3
20-30	788	3.8
30-40	644	3.1
40-50	510	2.5
50-60	409	2.0
60-70	358	1.7
70-80	376	1.8
80-90	283	1.4
90-100	317	1.5
> 100	7189	34.6

PARRIS

PARRIS usage summary as of Tue Oct 22 00:01:30 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 30 30 30-30 238 238 238-238 79 79 79-79

Last 30 days 6 0.20 23.67 23.50 9-38 882.50 285 227-3957 666.50 122.50 30-3448

Lifetime (4465 days) 14428 3.23 20.12 15 3-75 486.00 329 7-11903 426.76 137 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	1	0.14	30	30	30-30	238	238	238-238	79	79	79-79
Last 30 days	6	0.20	23.67	23.50	9-38	882.50	285	227-3957	666.50	122.50	30-3448
Lifetime (4465 days)	14428	3.23	20.12	15	3-75	486.00	329	7-11903	426.76	137	1-48648

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8168	56.6
F81	1068	7.4
REV	1008	7.0
TRN93	758	5.3
010000	429	3.0
012012	259	1.8
001101	166	1.2
012212	155	1.1
012032	129	0.9
010230	125	0.9

p-values range	Times found	% found
0-0.1	2627	18.2
0.1-0.2	513	3.6
0.2-0.3	465	3.2
0.3-0.4	365	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	8654	60.0

GA Branch

GABranch usage summary as of Tue Oct 22 00:01:32 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 2 0.07 30 30 30-30 3958 3958 3958-3958 400934.50 400934.50 366199-435670

Lifetime (4458 days) 11729 2.63 13.73 12 3-30 519.95 332 9-11628 5663.09 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	0
Last 30 days	2	0.07	30	30	30-30	3958	3958	3958-3958	400934.50	400934.50	366199-435670
Lifetime (4458 days)	11729	2.63	13.73	12	3-30	519.95	332	9-11628	5663.09	1521	1-889396

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8456	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	117	1.0
8	38	0.3
9	25	0.2

CMS

CMS usage summary as of Tue Oct 22 00:01:34 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 4 0.57 37.50 41.50 14-53 707.25 888 158-895 399020.50 343172 11952-897786

Last 30 days 6 0.20 44.67 42.50 14-86 794.67 888 158-1364 277330.50 48692 11952-897786

Lifetime (3549 days) 3205 0.90 33.71 24 3-120 563.81 340 7-11276 21213.84 4067 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	4	0.57	37.50	41.50	14-53	707.25	888	158-895	399020.50	343172	11952-897786
Last 30 days	6	0.20	44.67	42.50	14-86	794.67	888	158-1364	277330.50	48692	11952-897786
Lifetime (3549 days)	3205	0.90	33.71	24	3-120	563.81	340	7-11276	21213.84	4067	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	178	5.6
60-70	174	5.4
70-80	128	4.0
80-90	175	5.5
90-100	108	3.4
> 100	1462	45.6

Number of rate classes	Times found	% found
1	0	0.0
2	2015	62.9
3	707	22.1
4	272	8.5
5	111	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 Tue Oct 22 00:01:35 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 2 0.07 64 64 32-96 2388 2388 1240-3536 531 531 393-669

Lifetime (3428 days) 3406 0.99 35.23 30 3-100 653.20 501 9-11100 500.87 139.50 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	2	0.07	64	64	32-96	2388	2388	1240-3536	531	531	393-669
Lifetime (3428 days)	3406	0.99	35.23	30	3-100	653.20	501	9-11100	500.87	139.50	2-31585

Subtyping

SCUEAL usage summary as of Tue Oct 22 00:01:37 2019 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 6397 6397.00 81.91 4 0-500

Last 7 days 6397 913.86 81.91 4 0-500

Last 30 days 6397 213.23 81.91 4 0-500

Lifetime (3763 days) 7701 2.05 86.98 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	6397	6397.00	81.91	4	0-500
Last 7 days	6397	913.86	81.91	4	0-500
Last 30 days	6397	213.23	81.91	4	0-500
Lifetime (3763 days)	7701	2.05	86.98	5	0-500

Top 10 Subtypes (out of 669802 sequences)

Subtypes Times found % found

B 261048 39.0

C 116502 17.4

G 46059 6.9

A1 42000 6.3

Complex 28191 4.2

AE 19805 3.0

D 18956 2.8

CRF14 11763 1.8

F1 10612 1.6

B,C recombinant 9163 1.4

Subtypes	Times found	% found
B	261048	39.0
C	116502	17.4
G	46059	6.9
A1	42000	6.3
Complex	28191	4.2
AE	19805	3.0
D	18956	2.8
CRF14	11763	1.8
F1	10612	1.6
B,C recombinant	9163	1.4

Coevolution

BGM usage summary as of Tue Oct 22 00:01:39 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 (2357 days) 8881 3.77 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 (2357 days)	8881	3.77	65.10	30	0-1033	2.25	0.98	0.01-263	2866.47	92	0-2900666

UCSD Viral Evolution Group 2004-2019