Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Wed Apr 24 00:00:02 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 266 8.87 146.10 90 3-492 594.85 467.50 60-3958 39.68 17.88 0.26- 191.60

Lifetime (3076 days) 92479 30.06 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	266	8.87	146.10	90	3-492	594.85	467.50	60-3958	39.68	17.88	0.26- 191.60
Lifetime (3076 days)	92479	30.06	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 Wed Apr 24 00:00:14 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 5 5 5-5 461 461 461-461 301 301 301-301

Last 7 days 32 4.57 54 9 4-278 668.12 738 174-2036 714.81 440.50 110-3671

Last 30 days 282 9.40 40.54 23 3-297 678.90 460 41-3958 1156.15 324.50 5-14810

Lifetime (2176 days) 101334 46.57 44.23 24 3-787 483.17 325 1-11276 148.26 45 0-26278

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	5	5	5-5	461	461	461-461	301	301	301-301
Last 7 days	32	4.57	54	9	4-278	668.12	738	174-2036	714.81	440.50	110-3671
Last 30 days	282	9.40	40.54	23	3-297	678.90	460	41-3958	1156.15	324.50	5-14810
Lifetime (2176 days)	101334	46.57	44.23	24	3-787	483.17	325	1-11276	148.26	45	0-26278

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 45657 45.1
REV 13160 13.0
TRN93 9984 9.9
F81 5215 5.1
010000 3926 3.9
010232 2074 2.0
012012 1557 1.5
012212 1372 1.4
010230 1228 1.2
012032 989 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 24.1 81940 80.9
0.05 0.9 19.2 15005 14.8
0.2 2.1 30.0 2069 2.0
0.25 3.1 32.5 909 0.9
0.01 0.4 14.7 520 0.5
0.5 5.9 42.7 212 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 Wed Apr 24 00:00:28 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 5 5 5-5 461 461 461-461 63 63 63-63

Last 7 days 34 4.86 13.38 5 4-58 795.65 742 174-2321 218.15 66.50 15-1196

Last 30 days 118 3.93 20.26 15 3-75 722.07 588.50 6-3392 1895.56 270.50 12-40807

Lifetime (2175 days) 56296 25.88 20.63 16 2-110 485.26 322 1-10798 381.21 109 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	5	5	5-5	461	461	461-461	63	63	63-63
Last 7 days	34	4.86	13.38	5	4-58	795.65	742	174-2321	218.15	66.50	15-1196
Last 30 days	118	3.93	20.26	15	3-75	722.07	588.50	6-3392	1895.56	270.50	12-40807
Lifetime (2175 days)	56296	25.88	20.63	16	2-110	485.26	322	1-10798	381.21	109	0-54132

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 29759 52.9
REV 5632 10.0
F81 3319 5.9
TRN93 3315 5.9
010000 2336 4.1
012012 1182 2.1
001101 727 1.3
012212 699 1.2
010232 694 1.2
012032 603 1.1

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

50 4.3 27.8 50884 90.4
100 4.3 22.5 1297 2.3
90 19.2 11.2 900 1.6
20 7.2 36.0 819 1.5
10 5.8 31.7 744 1.3
95 2.2 30.7 700 1.2
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 Wed Apr 24 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 0

Last 7 days 0

Last 30 days 2 0.07 63 63 24-102 207 207 201-213 17480.50 17480.50 2781-32180

Lifetime (3256 days) 1075 0.33 47.54 37 7-150 568.81 350 16-3789 3782.81 1968 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	2	0.07	63	63	24-102	207	207	201-213	17480.50	17480.50	2781-32180
Lifetime (3256 days)	1075	0.33	47.54	37	7-150	568.81	350	16-3789	3782.81	1968	31-42841

Model Select.

ModelSelection usage summary as of Wed Apr 24 00:00:35 2019 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 12 12.00 52.25 8 7-461 342.83 233 97-758

Last 7 days 38 5.43 36.82 20.50 4-461 514.32 273 97-2036

Last 30 days 325 10.83 143.19 87 3-499 603.58 498 6-3392

Lifetime (2176 days) 99483 45.72 43.04 22 3-656 518.32 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	12	12.00	52.25	8	7-461	342.83	233	97-758
Last 7 days	38	5.43	36.82	20.50	4-461	514.32	273	97-2036
Last 30 days	325	10.83	143.19	87	3-499	603.58	498	6-3392
Lifetime (2176 days)	99483	45.72	43.04	22	3-656	518.32	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 23932 24.1
TRN93 12888 13.0
F81 8625 8.7
010232 4295 4.3
012012 3432 3.4
012212 2982 3.0
010230 2381 2.4
012232 2358 2.4
012032 2355 2.4
001101 2083 2.1

Model	Times selected	% selected
HKY85	23932	24.1
TRN93	12888	13.0
F81	8625	8.7
010232	4295	4.3
012012	3432	3.4
012212	2982	3.0
010230	2381	2.4
012232	2358	2.4
012032	2355	2.4
001101	2083	2.1

Protein Model Select.

ModelSelectionP usage summary as of Wed Apr 24 00:00:44 2019 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 2 2.00 55 55 10-100 976 976 233-1719

Last 7 days 2 0.29 55 55 10-100 976 976 233-1719

Last 30 days 9 0.30 87.33 57 10-223 416.33 216 210-1719

Lifetime (3977 days) 3835 0.96 46.10 25 2-499 651.04 444 3-18120

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	2	2.00	55	55	10-100	976	976	233-1719
Last 7 days	2	0.29	55	55	10-100	976	976	233-1719
Last 30 days	9	0.30	87.33	57	10-223	416.33	216	210-1719
Lifetime (3977 days)	3835	0.96	46.10	25	2-499	651.04	444	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 559 14.6
JTT (Jones,Taylor,Thornton) 404 10.5
BLOSUM62+F 324 8.4
WAG (Whelan and Goldman)+F 319 8.3
WAG (Whelan and Goldman) 244 6.4
HIV (within host)+F 241 6.3
IAV (Influenza A virus)+F 238 6.2
IAV (Influenza A virus) 223 5.8
BLOSUM62 167 4.4
LG (Le and Gascuel) 161 4.2

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)+F	559	14.6
JTT (Jones,Taylor,Thornton)	404	10.5
BLOSUM62+F	324	8.4
WAG (Whelan and Goldman)+F	319	8.3
WAG (Whelan and Goldman)	244	6.4
HIV (within host)+F	241	6.3
IAV (Influenza A virus)+F	238	6.2
IAV (Influenza A virus)	223	5.8
BLOSUM62	167	4.4
LG (Le and Gascuel)	161	4.2

GARD

GARD usage summary as of Wed Apr 24 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 0

Last 7 days 0

Last 30 days 32 1.07 46.19 19 3-139 1639.50 1558.50 348-5922 2562.66 2709 138-7560

Lifetime (4529 days) 74794 16.51 26.85 18 2-300 2033.26 1113 20-46625 1281.00 378 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	32	1.07	46.19	19	3-139	1639.50	1558.50	348-5922	2562.66	2709	138-7560
Lifetime (4529 days)	74794	16.51	26.85	18	2-300	2033.26	1113	20-46625	1281.00	378	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	63105	84.4
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	27168	36.3
10-20	2988	4.0
20-30	2412	3.2
30-40	2239	3.0
40-50	1845	2.5
50-60	1949	2.6
60-70	1422	1.9
70-80	1312	1.8
80-90	1213	1.6
90-100	1077	1.4
> 100	31169	41.7

Number of breakpoints	Times found	% found
0	22839	30.5
1	18951	25.3
2	11864	15.9
3	6880	9.2
4	4186	5.6
5	2888	3.9
6	1869	2.5
7	1407	1.9
8	934	1.2
9	761	1.0
≥ 10	2215	3.0

SBP

SBP usage summary as of Wed Apr 24 00:00:55 2019 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 37 37 32-42 1 1 1-1 423.50 423.50 134-713

Last 7 days 11 1.57 54.36 40 9-201 6 1 1-33 434.82 217 48-1661

Last 30 days 58 1.93 157.05 76 4-388 7.29 3.50 1-39 3421.74 1574.50 10-21911

Lifetime (2176 days) 20576 9.46 49.39 24 2-656 21.75 1 1-45015 566.95 41 0-683633

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	37	37	32-42	1	1	1-1	423.50	423.50	134-713
Last 7 days	11	1.57	54.36	40	9-201	6	1	1-33	434.82	217	48-1661
Last 30 days	58	1.93	157.05	76	4-388	7.29	3.50	1-39	3421.74	1574.50	10-21911
Lifetime (2176 days)	20576	9.46	49.39	24	2-656	21.75	1	1-45015	566.95	41	0-683633

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	14853	72.2
REV	1315	6.4
010000	565	2.7
F81	503	2.4
TRN93	502	2.4
0123455	228	1.1
010232	215	1.0
012012	137	0.7
0112304567	115	0.6
010230	105	0.5

IC improvement range	Times found	% found
0-10	8900	43.3
10-20	897	4.4
20-30	788	3.8
30-40	636	3.1
40-50	508	2.5
50-60	406	2.0
60-70	353	1.7
70-80	374	1.8
80-90	282	1.4
90-100	311	1.5
> 100	7121	34.6

PARRIS

PARRIS usage summary as of Wed Apr 24 00:00:58 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 30.11 40 4-58 518.22 509 174-1145 240.33 196 7-844

Last 30 days 66 2.20 13.42 8 3-58 453.68 341.50 116-1997 599.11 151 7-14723

Lifetime (4284 days) 14337 3.35 20.15 15 3-75 486.27 329 7-11903 424.22 137 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	9	1.29	30.11	40	4-58	518.22	509	174-1145	240.33	196	7-844
Last 30 days	66	2.20	13.42	8	3-58	453.68	341.50	116-1997	599.11	151	7-14723
Lifetime (4284 days)	14337	3.35	20.15	15	3-75	486.27	329	7-11903	424.22	137	1-48648

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8119	56.6
F81	1064	7.4
REV	1003	7.0
TRN93	751	5.2
010000	429	3.0
012012	252	1.8
001101	166	1.2
012212	154	1.1
012032	128	0.9
010230	121	0.8

p-values range	Times found	% found
0-0.1	2621	18.3
0.1-0.2	510	3.6
0.2-0.3	463	3.2
0.3-0.4	363	2.5
0.4-0.5	330	2.3
0.5-0.6	389	2.7
0.6-0.7	367	2.6
0.7-0.8	357	2.5
0.8-0.9	350	2.4
0.9-1	8587	59.9

GA Branch

GABranch usage summary as of Wed Apr 24 00:01:00 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 6.50 6.50 4-9 507.50 507.50 273-742 1064 1064 8-2120

Last 30 days 9 0.30 15 14 4-27 352.22 339 51-742 12479.56 2120 8-57340

Lifetime (4277 days) 11702 2.74 13.73 12 3-30 518.59 331 9-11628 5559.51 1518.50 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	2	0.29	6.50	6.50	4-9	507.50	507.50	273-742	1064	1064	8-2120
Last 30 days	9	0.30	15	14	4-27	352.22	339	51-742	12479.56	2120	8-57340
Lifetime (4277 days)	11702	2.74	13.73	12	3-30	518.59	331	9-11628	5559.51	1518.50	1-889396

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8431	72.0
REV	614	5.2
010000	568	4.9
F81	415	3.5
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	4274	36.5
3	3953	33.8
4	2196	18.8
5	771	6.6
6	233	2.0
7	116	1.0
8	36	0.3
9	24	0.2

CMS

CMS usage summary as of Wed Apr 24 00:01:02 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 9 9 9-9 273 273 273-273 2504 2504 2504-2504

Last 7 days 5 0.71 19.20 9 9-40 354.40 273 177-776 21246.20 3560 2504-51705

Last 30 days 16 0.53 23.94 20.50 3-77 635.19 529.50 177-3352 22322.56 19351 724-51705

Lifetime (3368 days) 3174 0.94 33.69 24 3-120 554.95 340 7-11276 18708.58 4011 59-2971964

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	9	9	9-9	273	273	273-273	2504	2504	2504-2504
Last 7 days	5	0.71	19.20	9	9-40	354.40	273	177-776	21246.20	3560	2504-51705
Last 30 days	16	0.53	23.94	20.50	3-77	635.19	529.50	177-3352	22322.56	19351	724-51705
Lifetime (3368 days)	3174	0.94	33.69	24	3-120	554.95	340	7-11276	18708.58	4011	59-2971964

Distribution of mBIC improvement

Number of inferred rate classes

mBIC improvement range	Times found	% found
0-10	184	5.8
10-20	146	4.6
20-30	188	5.9
30-40	215	6.8
40-50	243	7.7
50-60	178	5.6
60-70	173	5.5
70-80	127	4.0
80-90	175	5.5
90-100	108	3.4
> 100	1437	45.3

Number of rate classes	Times found	% found
1	0	0.0
2	2004	63.1
3	700	22.1
4	265	8.3
5	107	3.4
6	48	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 Apr 24 00:01:02 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 70.67 74 59-79 313 378 183-378 438 440 308-566

Last 30 days 8 0.27 48 46 10-79 246.12 211 183-378 362.62 346 193-566

Lifetime (3247 days) 3119 0.96 34.18 27 3-100 617.87 481 9-11100 510.63 126 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	3	0.43	70.67	74	59-79	313	378	183-378	438	440	308-566
Last 30 days	8	0.27	48	46	10-79	246.12	211	183-378	362.62	346	193-566
Lifetime (3247 days)	3119	0.96	34.18	27	3-100	617.87	481	9-11100	510.63	126	2-31585

Subtyping

SCUEAL usage summary as of Wed Apr 24 00:01:03 2019 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 6093 6093.00 83.44 4 0-500

Last 7 days 6093 870.43 83.44 4 0-500

Last 30 days 6093 203.10 83.44 4 0-500

Lifetime (3582 days) 7397 2.07 88.45 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	6093	6093.00	83.44	4	0-500
Last 7 days	6093	870.43	83.44	4	0-500
Last 30 days	6093	203.10	83.44	4	0-500
Lifetime (3582 days)	7397	2.07	88.45	5	0-500

Top 10 Subtypes (out of 654241 sequences)

Subtypes Times found % found

B 257158 39.3

C 111230 17.0

G 45899 7.0

A1 41324 6.3

Complex 26969 4.1

AE 19222 2.9

D 18758 2.9

CRF14 11742 1.8

F1 10465 1.6

B,C recombinant 8469 1.3

Subtypes	Times found	% found
B	257158	39.3
C	111230	17.0
G	45899	7.0
A1	41324	6.3
Complex	26969	4.1
AE	19222	2.9
D	18758	2.9
CRF14	11742	1.8
F1	10465	1.6
B,C recombinant	8469	1.3

Coevolution

BGM usage summary as of Wed Apr 24 00:01:05 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 (2176 days) 8881 4.08 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 (2176 days)	8881	4.08	65.10	30	0-1033	2.25	0.98	0.01-263	2866.47	92	0-2900666

UCSD Viral Evolution Group 2004-2019