Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Wed Oct 17 00:00:01 2018 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 15 15.00 29.20 21 3-115 327.67 235 81-820 5.21 1.96 0.37- 18.89

Last 7 days 161 23.00 38.10 15 3-486 428.51 219 52-3721 8.32 2.25 0.29- 84.29

Last 30 days 547 18.23 55.52 18 3-499 407.96 298 6-4390 12.12 2.43 0.23- 209.14

Lifetime (2887 days) 89762 31.09 52.09 25 3-684 488.48 325 1-11903 21.26 6.18 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	15	15.00	29.20	21	3-115	327.67	235	81-820	5.21	1.96	0.37- 18.89
Last 7 days	161	23.00	38.10	15	3-486	428.51	219	52-3721	8.32	2.25	0.29- 84.29
Last 30 days	547	18.23	55.52	18	3-499	407.96	298	6-4390	12.12	2.43	0.23- 209.14
Lifetime (2887 days)	89762	31.09	52.09	25	3-684	488.48	325	1-11903	21.26	6.18	0.16- 7571.98

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 46375 51.7
TRN93 13237 14.7
REV 9420 10.5
F81 4047 4.5
010230 1039 1.2
010232 992 1.1
012212 967 1.1
012012 926 1.0
012232 779 0.9
010210 693 0.8

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 0.6 16.2 75146 83.7
0.05 0.5 14.5 10912 12.2
0.2 0.9 18.1 1359 1.5
0.25 2.2 25.3 751 0.8
0.5 4.4 55.7 617 0.7
0.01 0.8 9.4 527 0.6
0.15 2.5 15.0 103 0.1
0.3 0.2 19.2 47 0.1
0.0024 0.0 2.3 45 0.1
0.0048 0.0 0.5 33 0.0

FEL

FEL usage summary as of Wed Oct 17 00:00:12 2018 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 68.67 69 25-115 603.67 610 235-820 278.50 256 185-442

Last 7 days 84 12.00 37.61 17 10-499 503.15 417 52-3721 260.86 63 7-4353

Last 30 days 315 10.50 31.26 17 3-499 398.39 301 10-3721 133.57 50 4-4353

Lifetime (1987 days) 99357 50.00 44.24 24 3-787 479.23 325 1-11276 140.61 44 0-26278

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	68.67	69	25-115	603.67	610	235-820	278.50	256	185-442
Last 7 days	84	12.00	37.61	17	10-499	503.15	417	52-3721	260.86	63	7-4353
Last 30 days	315	10.50	31.26	17	3-499	398.39	301	10-3721	133.57	50	4-4353
Lifetime (1987 days)	99357	50.00	44.24	24	3-787	479.23	325	1-11276	140.61	44	0-26278

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 44648 44.9
REV 13005 13.1
TRN93 9825 9.9
F81 4991 5.0
010000 3923 3.9
010232 2047 2.1
012012 1471 1.5
012212 1342 1.4
010230 1217 1.2
012032 964 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 24.2 80328 80.8
0.05 0.9 19.2 14792 14.9
0.2 2.1 29.6 2036 2.0
0.25 3.2 33.0 876 0.9
0.01 0.5 14.3 504 0.5
0.5 5.4 43.6 198 0.2
0.15 2.6 22.7 154 0.2
0.0024 0.0 7.0 102 0.1
0.3 1.2 22.3 63 0.1
0.0004 0.0 6.6 29 0.0

REL

REL usage summary as of Wed Oct 17 00:00:25 2018 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 5 5.00 29.80 31 23-35 800.40 820 672-891 226.40 197 173-373

Last 7 days 60 8.57 21.80 16.50 10-75 523.80 414.50 52-5285 260.45 117 10-2626

Last 30 days 181 6.03 23.52 17 3-75 394.36 271 10-5285 208.12 92 1-2626

Lifetime (1986 days) 55299 27.84 20.63 16 2-110 481.70 319 1-10798 366.21 108 0-39109

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	5	5.00	29.80	31	23-35	800.40	820	672-891	226.40	197	173-373
Last 7 days	60	8.57	21.80	16.50	10-75	523.80	414.50	52-5285	260.45	117	10-2626
Last 30 days	181	6.03	23.52	17	3-75	394.36	271	10-5285	208.12	92	1-2626
Lifetime (1986 days)	55299	27.84	20.63	16	2-110	481.70	319	1-10798	366.21	108	0-39109

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 29248 52.9
REV 5620 10.2
TRN93 3258 5.9
F81 3187 5.8
010000 2336 4.2
012012 1095 2.0
001101 725 1.3
010232 687 1.2
012212 674 1.2
012032 577 1.0

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

50 4.3 27.8 49945 90.3
100 4.2 22.6 1285 2.3
90 19.4 11.1 890 1.6
20 7.3 36.2 808 1.5
10 5.7 31.8 735 1.3
95 2.2 30.8 694 1.3
40 2.5 24.4 145 0.3
80 3.0 28.5 107 0.2
30 10.0 20.2 91 0.2
25 2.3 37.1 85 0.2

TOGGLE

Toggle usage summary as of Wed Oct 17 00:00:31 2018 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 58 58 58-58 174 174 174-174 310 310 310-310

Lifetime (3067 days) 1068 0.35 47.53 37 7-150 565.40 350 16-3789 3756.52 1919.50 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	58	58	58-58	174	174	174-174	310	310	310-310
Lifetime (3067 days)	1068	0.35	47.53	37	7-150	565.40	350	16-3789	3756.52	1919.50	31-42841

Model Select.

ModelSelection usage summary as of Wed Oct 17 00:00:32 2018 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 20 20.00 29.55 21 3-115 349.17 186.50 75-820

Last 7 days 140 20.00 33.37 18 3-207 478.02 289.50 52-5285

Last 30 days 473 15.77 52.58 18 3-484 415.27 298 10-5285

Lifetime (1987 days) 96715 48.67 41.90 22 3-656 515.75 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	20	20.00	29.55	21	3-115	349.17	186.50	75-820
Last 7 days	140	20.00	33.37	18	3-207	478.02	289.50	52-5285
Last 30 days	473	15.77	52.58	18	3-484	415.27	298	10-5285
Lifetime (1987 days)	96715	48.67	41.90	22	3-656	515.75	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 23296 24.1
TRN93 12706 13.1
F81 8428 8.7
010232 4234 4.4
012012 3231 3.3
012212 2874 3.0
010230 2301 2.4
012032 2214 2.3
012232 2182 2.3
001101 2053 2.1

Model	Times selected	% selected
HKY85	23296	24.1
TRN93	12706	13.1
F81	8428	8.7
010232	4234	4.4
012012	3231	3.3
012212	2874	3.0
010230	2301	2.4
012032	2214	2.3
012232	2182	2.3
001101	2053	2.1

Protein Model Select.

ModelSelectionP usage summary as of Wed Oct 17 00:00:41 2018 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 1 0.14 15 15 15-15 136 136 136-136

Last 30 days 3 0.10 21.67 15 15-35 239.67 223 136-360

Lifetime (3788 days) 3779 1.00 45.96 25 2-499 652.40 444 3-18120

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	1	0.14	15	15	15-15	136	136	136-136
Last 30 days	3	0.10	21.67	15	15-35	239.67	223	136-360
Lifetime (3788 days)	3779	1.00	45.96	25	2-499	652.40	444	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 550 14.6
JTT (Jones,Taylor,Thornton) 400 10.6
BLOSUM62+F 318 8.4
WAG (Whelan and Goldman)+F 311 8.2
WAG (Whelan and Goldman) 241 6.4
IAV (Influenza A virus)+F 235 6.2
HIV (within host)+F 235 6.2
IAV (Influenza A virus) 217 5.7
BLOSUM62 165 4.4
LG (Le and Gascuel) 161 4.3

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)+F	550	14.6
JTT (Jones,Taylor,Thornton)	400	10.6
BLOSUM62+F	318	8.4
WAG (Whelan and Goldman)+F	311	8.2
WAG (Whelan and Goldman)	241	6.4
IAV (Influenza A virus)+F	235	6.2
HIV (within host)+F	235	6.2
IAV (Influenza A virus)	217	5.7
BLOSUM62	165	4.4
LG (Le and Gascuel)	161	4.3

GARD

GARD usage summary as of Wed Oct 17 00:00:42 2018 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 6 0.86 41.17 32 18-75 1161 1059 408-2358 1532.67 888 316-4225

Last 30 days 25 0.83 54.72 37 7-156 2196.52 1269 231-8359 2376.24 900 68-9511

Lifetime (4340 days) 74081 17.07 26.87 18 2-300 2028.85 1110 20-46625 1270.54 374 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	6	0.86	41.17	32	18-75	1161	1059	408-2358	1532.67	888	316-4225
Last 30 days	25	0.83	54.72	37	7-156	2196.52	1269	231-8359	2376.24	900	68-9511
Lifetime (4340 days)	74081	17.07	26.87	18	2-300	2028.85	1110	20-46625	1270.54	374	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	62392	84.2
HKY85	5991	8.1
010000	860	1.2
REV	830	1.1
TRN93	558	0.8
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	26907	36.3
10-20	2950	4.0
20-30	2390	3.2
30-40	2219	3.0
40-50	1826	2.5
50-60	1943	2.6
60-70	1405	1.9
70-80	1301	1.8
80-90	1195	1.6
90-100	1071	1.4
> 100	30874	41.7

Number of breakpoints	Times found	% found
0	22618	30.5
1	18785	25.4
2	11740	15.8
3	6782	9.2
4	4132	5.6
5	2852	3.8
6	1855	2.5
7	1407	1.9
8	934	1.3
9	761	1.0
≥ 10	2215	3.0

SBP

SBP usage summary as of Wed Oct 17 00:00:51 2018 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 30.50 30.50 22-39 5.50 5.50 3-8 21.50 21.50 2-41

Last 30 days 14 0.47 45.79 40 12-151 18.57 1 1-203 289.93 80 0-1041

Lifetime (1987 days) 20341 10.24 48.86 24 2-656 21.72 1 1-45015 477.24 41 0-279793

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	30.50	30.50	22-39	5.50	5.50	3-8	21.50	21.50	2-41
Last 30 days	14	0.47	45.79	40	12-151	18.57	1	1-203	289.93	80	0-1041
Lifetime (1987 days)	20341	10.24	48.86	24	2-656	21.72	1	1-45015	477.24	41	0-279793

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	14629	71.9
REV	1315	6.5
010000	565	2.8
TRN93	501	2.5
F81	501	2.5
0123455	227	1.1
010232	215	1.1
012012	137	0.7
0112304567	115	0.6
010230	105	0.5

IC improvement range	Times found	% found
0-10	8788	43.2
10-20	892	4.4
20-30	780	3.8
30-40	629	3.1
40-50	504	2.5
50-60	403	2.0
60-70	351	1.7
70-80	374	1.8
80-90	281	1.4
90-100	300	1.5
> 100	7039	34.6

PARRIS

PARRIS usage summary as of Wed Oct 17 00:00:55 2018 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 2 2.00 25 25 23-27 805.50 805.50 720-891 500.50 500.50 240-761

Last 7 days 6 0.86 22 21 18-27 774.33 868 154-1018 396.50 236.50 196-761

Last 30 days 15 0.50 20.93 18 9-58 675.40 845 154-1049 236.13 196 61-761

Lifetime (4095 days) 14229 3.47 20.18 15 3-75 484.64 329 7-11903 413.92 136 1-35284

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	2	2.00	25	25	23-27	805.50	805.50	720-891	500.50	500.50	240-761
Last 7 days	6	0.86	22	21	18-27	774.33	868	154-1018	396.50	236.50	196-761
Last 30 days	15	0.50	20.93	18	9-58	675.40	845	154-1049	236.13	196	61-761
Lifetime (4095 days)	14229	3.47	20.18	15	3-75	484.64	329	7-11903	413.92	136	1-35284

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8034	56.5
F81	1061	7.5
REV	1000	7.0
TRN93	745	5.2
010000	429	3.0
012012	251	1.8
001101	166	1.2
012212	153	1.1
012032	127	0.9
010230	120	0.8

p-values range	Times found	% found
0-0.1	2606	18.3
0.1-0.2	504	3.5
0.2-0.3	460	3.2
0.3-0.4	361	2.5
0.4-0.5	326	2.3
0.5-0.6	389	2.7
0.6-0.7	364	2.6
0.7-0.8	353	2.5
0.8-0.9	349	2.5
0.9-1	8517	59.9

GA Branch

GABranch usage summary as of Wed Oct 17 00:00:56 2018 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 14 14 12-16 503.50 503.50 122-885 7564.50 7564.50 4760-10369

Last 30 days 2 0.07 14 14 12-16 503.50 503.50 122-885 7564.50 7564.50 4760-10369

Lifetime (4088 days) 11663 2.85 13.72 12 3-30 515.93 330 9-11628 5301.91 1513 1-636439

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	14	14	12-16	503.50	503.50	122-885	7564.50	7564.50	4760-10369
Last 30 days	2	0.07	14	14	12-16	503.50	503.50	122-885	7564.50	7564.50	4760-10369
Lifetime (4088 days)	11663	2.85	13.72	12	3-30	515.93	330	9-11628	5301.91	1513	1-636439

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8392	72.0
REV	614	5.3
010000	568	4.9
F81	415	3.6
TRN93	283	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	4259	36.5
3	3946	33.8
4	2191	18.8
5	766	6.6
6	231	2.0
7	113	1.0
8	35	0.3
9	23	0.2

CMS

CMS usage summary as of Wed Oct 17 00:00:58 2018 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 3 0.10 48.33 49 38-58 130.33 140 77-174 9872 7335 3707-18574

Lifetime (3179 days) 3119 0.98 33.67 24 3-120 536.34 338 7-11276 17733.73 3905 59-2971964

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	3	0.10	48.33	49	38-58	130.33	140	77-174	9872	7335	3707-18574
Lifetime (3179 days)	3119	0.98	33.67	24	3-120	536.34	338	7-11276	17733.73	3905	59-2971964

Distribution of mBIC improvement

Number of inferred rate classes

mBIC improvement range	Times found	% found
0-10	183	5.9
10-20	143	4.6
20-30	188	6.0
30-40	213	6.8
40-50	239	7.7
50-60	175	5.6
60-70	170	5.5
70-80	127	4.1
80-90	172	5.5
90-100	107	3.4
> 100	1402	45.0

Number of rate classes	Times found	% found
1	0	0.0
2	1977	63.4
3	686	22.0
4	256	8.2
5	104	3.3
6	46	1.5
7	14	0.4
8	2	0.1
9	0	0.0
≥ 10	34	1.1

DEPS

DEPS usage summary as of Wed Oct 17 00:00:59 2018 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 13 0.43 59.54 59 33-97 389.77 230 223-757 4217.54 1263 73-19670

Lifetime (3058 days) 3050 1.00 33.70 27 3-100 620.82 483 9-11100 480.68 123.50 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	13	0.43	59.54	59	33-97	389.77	230	223-757	4217.54	1263	73-19670
Lifetime (3058 days)	3050	1.00	33.70	27	3-100	620.82	483	9-11100	480.68	123.50	2-31585

Subtyping

SCUEAL usage summary as of Wed Oct 17 00:01:00 2018 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 5919 5919.00 83.30 4 0-500

Last 7 days 5919 845.57 83.30 4 0-500

Last 30 days 5919 197.30 83.30 4 0-500

Lifetime (3393 days) 7223 2.13 88.46 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	5919	5919.00	83.30	4	0-500
Last 7 days	5919	845.57	83.30	4	0-500
Last 30 days	5919	197.30	83.30	4	0-500
Lifetime (3393 days)	7223	2.13	88.46	5	0-500

Top 10 Subtypes (out of 638914 sequences)

Subtypes Times found % found

B 250377 39.2

C 108903 17.0

G 45560 7.1

A1 40506 6.3

Complex 26146 4.1

D 18612 2.9

AE 18467 2.9

CRF14 11731 1.8

F1 10058 1.6

B,C recombinant 8145 1.3

Subtypes	Times found	% found
B	250377	39.2
C	108903	17.0
G	45560	7.1
A1	40506	6.3
Complex	26146	4.1
D	18612	2.9
AE	18467	2.9
CRF14	11731	1.8
F1	10058	1.6
B,C recombinant	8145	1.3

Coevolution

BGM usage summary as of Wed Oct 17 00:01:02 2018 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 1 0.14 9 9 9-9 0.33 0.33 0.33- 0.33 0 0 0-0

Last 30 days 13 0.43 25.38 10 3-154 2.35 1 0.15- 11.40 870.77 0 0-8766

Lifetime (1987 days) 8813 4.44 64.74 30 0-1033 2.25 0.98 0.01-263 2884.00 93 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	1	0.14	9	9	9-9	0.33	0.33	0.33- 0.33	0	0	0-0
Last 30 days	13	0.43	25.38	10	3-154	2.35	1	0.15- 11.40	870.77	0	0-8766
Lifetime (1987 days)	8813	4.44	64.74	30	0-1033	2.25	0.98	0.01-263	2884.00	93	0-2900666

UCSD Viral Evolution Group 2004-2018