Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Fri Feb 22 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 20 20.00 28 32 5-53 391.65 323 86-756 5.86 5.36 0.67- 32.23

Last 7 days 77 11.00 34.91 31 5-248 482.69 566 86-756 4.64 2.50 0.48- 42.37

Last 30 days 398 13.27 140.64 80 3-434 588.82 466 82-3391 31.79 8.88 0.26- 141.61

Lifetime (3015 days) 91720 30.42 52.78 25 3-684 490.00 325 1-11903 21.24 6.17 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	20	20.00	28	32	5-53	391.65	323	86-756	5.86	5.36	0.67- 32.23
Last 7 days	77	11.00	34.91	31	5-248	482.69	566	86-756	4.64	2.50	0.48- 42.37
Last 30 days	398	13.27	140.64	80	3-434	588.82	466	82-3391	31.79	8.88	0.26- 141.61
Lifetime (3015 days)	91720	30.42	52.78	25	3-684	490.00	325	1-11903	21.24	6.17	0.16- 7571.98

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 47105 51.4
TRN93 13415 14.6
REV 9497 10.4
F81 4209 4.6
012012 1071 1.2
010230 1070 1.2
012212 1031 1.1
010232 1003 1.1
012232 848 0.9
012032 755 0.8

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 0.6 16.2 76461 83.4
0.05 0.5 14.1 11418 12.4
0.2 0.9 18.4 1380 1.5
0.25 2.2 24.8 775 0.8
0.5 4.4 56.0 646 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 Fri Feb 22 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 13 13.00 24.77 21 5-43 426.69 323 226-664 130 49 19-435

Last 7 days 64 9.14 30.12 28 5-80 516.23 566 138-2061 107.38 44 19-808

Last 30 days 159 5.30 33.50 19 3-287 703.79 431 82-3391 177.06 46 5-2456

Lifetime (2115 days) 100570 47.55 44.26 24 3-787 481.82 325 1-11276 142.97 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	13	13.00	24.77	21	5-43	426.69	323	226-664	130	49	19-435
Last 7 days	64	9.14	30.12	28	5-80	516.23	566	138-2061	107.38	44	19-808
Last 30 days	159	5.30	33.50	19	3-287	703.79	431	82-3391	177.06	46	5-2456
Lifetime (2115 days)	100570	47.55	44.26	24	3-787	481.82	325	1-11276	142.97	44	0-26278

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 45202 44.9
REV 13083 13.0
TRN93 9929 9.9
F81 5159 5.1
010000 3926 3.9
010232 2058 2.0
012012 1549 1.5
012212 1365 1.4
010230 1223 1.2
012032 985 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 24.2 81280 80.8
0.05 0.9 19.1 14923 14.8
0.2 2.1 29.9 2063 2.1
0.25 3.2 32.7 898 0.9
0.01 0.4 14.7 520 0.5
0.5 5.9 42.8 207 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 Fri Feb 22 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 6 6.00 25.33 26.50 5-43 450.83 424.50 303-664 620.83 121.50 68-1901

Last 7 days 20 2.86 27.35 21.50 4-44 476.60 562 124-664 242.15 84.50 16-1901

Last 30 days 80 2.67 17.82 17.50 3-44 500.79 358 56-2032 223.51 82.50 3-2233

Lifetime (2114 days) 55965 26.47 20.62 16 2-110 483.96 321 1-10798 368.53 109 0-50486

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	25.33	26.50	5-43	450.83	424.50	303-664	620.83	121.50	68-1901
Last 7 days	20	2.86	27.35	21.50	4-44	476.60	562	124-664	242.15	84.50	16-1901
Last 30 days	80	2.67	17.82	17.50	3-44	500.79	358	56-2032	223.51	82.50	3-2233
Lifetime (2114 days)	55965	26.47	20.62	16	2-110	483.96	321	1-10798	368.53	109	0-50486

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 29565 52.8
REV 5630 10.1
TRN93 3290 5.9
F81 3278 5.9
010000 2336 4.2
012012 1172 2.1
001101 725 1.3
012212 693 1.2
010232 689 1.2
012032 595 1.1

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

50 4.3 27.8 50567 90.4
100 4.2 22.5 1296 2.3
90 19.4 11.1 890 1.6
20 7.2 36.0 819 1.5
10 5.8 31.7 741 1.3
95 2.2 30.7 700 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 Fri Feb 22 00:00:35 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 0

Lifetime (3195 days) 1072 0.34 47.53 37 7-150 569.79 350 16-3789 3752.07 1961.50 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 (3195 days)	1072	0.34	47.53	37	7-150	569.79	350	16-3789	3752.07	1961.50	31-42841

Model Select.

ModelSelection usage summary as of Fri Feb 22 00:00:36 2019 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 16 16.00 23.69 28 5-32 338.69 323 89-566

Last 7 days 31 4.43 21.06 21 5-35 393.52 323 46-2011

Last 30 days 323 10.77 164.00 113 3-434 538.52 448 46-11125

Lifetime (2115 days) 98759 46.69 42.65 22 3-656 517.71 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	16	16.00	23.69	28	5-32	338.69	323	89-566
Last 7 days	31	4.43	21.06	21	5-35	393.52	323	46-2011
Last 30 days	323	10.77	164.00	113	3-434	538.52	448	46-11125
Lifetime (2115 days)	98759	46.69	42.65	22	3-656	517.71	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 23764 24.1
TRN93 12830 13.0
F81 8570 8.7
010232 4269 4.3
012012 3419 3.5
012212 2952 3.0
010230 2356 2.4
012032 2334 2.4
012232 2321 2.4
001101 2072 2.1

Model	Times selected	% selected
HKY85	23764	24.1
TRN93	12830	13.0
F81	8570	8.7
010232	4269	4.3
012012	3419	3.5
012212	2952	3.0
010230	2356	2.4
012032	2334	2.4
012232	2321	2.4
001101	2072	2.1

Protein Model Select.

ModelSelectionP usage summary as of Fri Feb 22 00:00:45 2019 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 19 19 19-19 370 370 370-370

Last 30 days 6 0.20 39.17 19.50 13-146 525.17 546 293-730

Lifetime (3916 days) 3820 0.98 45.87 25 2-499 650.50 444 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	19	19	19-19	370	370	370-370
Last 30 days	6	0.20	39.17	19.50	13-146	525.17	546	293-730
Lifetime (3916 days)	3820	0.98	45.87	25	2-499	650.50	444	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 559 14.6
JTT (Jones,Taylor,Thornton) 403 10.5
BLOSUM62+F 323 8.5
WAG (Whelan and Goldman)+F 318 8.3
WAG (Whelan and Goldman) 244 6.4
IAV (Influenza A virus)+F 238 6.2
HIV (within host)+F 236 6.2
IAV (Influenza A virus) 218 5.7
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)	403	10.5
BLOSUM62+F	323	8.5
WAG (Whelan and Goldman)+F	318	8.3
WAG (Whelan and Goldman)	244	6.4
IAV (Influenza A virus)+F	238	6.2
HIV (within host)+F	236	6.2
IAV (Influenza A virus)	218	5.7
BLOSUM62	167	4.4
LG (Le and Gascuel)	161	4.2

GARD

GARD usage summary as of Fri Feb 22 00:00:47 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 23 28 5-31 734.25 546 267-1578 2125.75 2045 330-4083

Last 7 days 6 0.86 24.33 28 5-35 1141 1062 267-2220 2322.67 2716.50 330-4083

Last 30 days 68 2.27 16.01 11 3-49 2661.34 1240.50 168-10302 1668.40 1073.50 98-4083

Lifetime (4468 days) 74520 16.68 26.84 18 2-300 2029.15 1110.50 20-46625 1271.05 375 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	23	28	5-31	734.25	546	267-1578	2125.75	2045	330-4083
Last 7 days	6	0.86	24.33	28	5-35	1141	1062	267-2220	2322.67	2716.50	330-4083
Last 30 days	68	2.27	16.01	11	3-49	2661.34	1240.50	168-10302	1668.40	1073.50	98-4083
Lifetime (4468 days)	74520	16.68	26.84	18	2-300	2029.15	1110.50	20-46625	1271.05	375	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	62831	84.3
HKY85	5991	8.0
010000	860	1.2
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	27083	36.3
10-20	2985	4.0
20-30	2409	3.2
30-40	2237	3.0
40-50	1843	2.5
50-60	1946	2.6
60-70	1421	1.9
70-80	1311	1.8
80-90	1203	1.6
90-100	1076	1.4
> 100	31006	41.6

Number of breakpoints	Times found	% found
0	22765	30.5
1	18904	25.4
2	11802	15.8
3	6820	9.2
4	4164	5.6
5	2883	3.9
6	1865	2.5
7	1407	1.9
8	934	1.3
9	761	1.0
≥ 10	2215	3.0

SBP

SBP usage summary as of Fri Feb 22 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 0

Last 7 days 3 0.43 121.67 54 35-276 4.33 2 1-10 6190.67 970 113-17489

Last 30 days 13 0.43 42.31 16 7-276 10.85 2 1-96 1598.77 113 4-17489

Lifetime (2115 days) 20461 9.67 49.01 24 2-656 21.68 1 1-45015 480.02 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	3	0.43	121.67	54	35-276	4.33	2	1-10	6190.67	970	113-17489
Last 30 days	13	0.43	42.31	16	7-276	10.85	2	1-96	1598.77	113	4-17489
Lifetime (2115 days)	20461	9.67	49.01	24	2-656	21.68	1	1-45015	480.02	41	0-279793

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	14744	72.1
REV	1315	6.4
010000	565	2.8
F81	503	2.5
TRN93	502	2.5
0123455	228	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	8836	43.2
10-20	895	4.4
20-30	787	3.8
30-40	636	3.1
40-50	506	2.5
50-60	405	2.0
60-70	352	1.7
70-80	374	1.8
80-90	281	1.4
90-100	310	1.5
> 100	7079	34.6

PARRIS

PARRIS usage summary as of Fri Feb 22 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 1 1.00 7 7 7-7 86 86 86-86 85 85 85-85

Last 7 days 2 0.29 30.50 30.50 7-54 381.50 381.50 86-677 1198 1198 85-2311

Last 30 days 7 0.23 20.57 11 7-54 950.57 677 86-2032 663 360 64-2311

Lifetime (4223 days) 14258 3.38 20.18 15 3-75 485.62 329 7-11903 414.02 137 1-35284

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	86	86	86-86	85	85	85-85
Last 7 days	2	0.29	30.50	30.50	7-54	381.50	381.50	86-677	1198	1198	85-2311
Last 30 days	7	0.23	20.57	11	7-54	950.57	677	86-2032	663	360	64-2311
Lifetime (4223 days)	14258	3.38	20.18	15	3-75	485.62	329	7-11903	414.02	137	1-35284

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8049	56.5
F81	1063	7.5
REV	1001	7.0
TRN93	747	5.2
010000	429	3.0
012012	252	1.8
001101	166	1.2
012212	154	1.1
012032	128	0.9
010230	120	0.8

p-values range	Times found	% found
0-0.1	2608	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	2.4
0.9-1	8544	59.9

GA Branch

GABranch usage summary as of Fri Feb 22 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 1 1.00 16 16 16-16 520 520 520-520 10133 10133 10133-10133

Last 7 days 1 0.14 16 16 16-16 520 520 520-520 10133 10133 10133-10133

Last 30 days 4 0.13 12.75 12 11-16 1229 1276 332-2032 10470 11737 2927-15479

Lifetime (4216 days) 11683 2.77 13.72 12 3-30 516.67 330 9-11628 5304.11 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	1	1.00	16	16	16-16	520	520	520-520	10133	10133	10133-10133
Last 7 days	1	0.14	16	16	16-16	520	520	520-520	10133	10133	10133-10133
Last 30 days	4	0.13	12.75	12	11-16	1229	1276	332-2032	10470	11737	2927-15479
Lifetime (4216 days)	11683	2.77	13.72	12	3-30	516.67	330	9-11628	5304.11	1513	1-636439

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8412	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	4269	36.5
3	3949	33.8
4	2194	18.8
5	769	6.6
6	232	2.0
7	113	1.0
8	35	0.3
9	23	0.2

CMS

CMS usage summary as of Fri Feb 22 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 2 2.00 32 32 32-32 323 323 323-323 10124 10124 8763-11485

Last 7 days 2 0.29 32 32 32-32 323 323 323-323 10124 10124 8763-11485

Last 30 days 8 0.27 23.62 26 11-39 2337.75 1098.50 323-11125 22734.25 10835.50 4733-71649

Lifetime (3307 days) 3144 0.95 33.69 24 3-120 542.31 338 7-11276 17725.91 3942 59-2971964

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	32	32	32-32	323	323	323-323	10124	10124	8763-11485
Last 7 days	2	0.29	32	32	32-32	323	323	323-323	10124	10124	8763-11485
Last 30 days	8	0.27	23.62	26	11-39	2337.75	1098.50	323-11125	22734.25	10835.50	4733-71649
Lifetime (3307 days)	3144	0.95	33.69	24	3-120	542.31	338	7-11276	17725.91	3942	59-2971964

Distribution of mBIC improvement

Number of inferred rate classes

mBIC improvement range	Times found	% found
0-10	184	5.9
10-20	146	4.6
20-30	188	6.0
30-40	214	6.8
40-50	240	7.6
50-60	177	5.6
60-70	170	5.4
70-80	127	4.0
80-90	175	5.6
90-100	108	3.4
> 100	1415	45.0

Number of rate classes	Times found	% found
1	0	0.0
2	1993	63.4
3	693	22.0
4	256	8.1
5	106	3.4
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 Fri Feb 22 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 0

Last 30 days 9 0.30 33.56 20 13-90 617.78 535 288-1199 450.11 206 84-1507

Lifetime (3186 days) 3107 0.98 34.08 27 3-100 618.34 482 9-11100 502.84 125 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	9	0.30	33.56	20	13-90	617.78	535	288-1199	450.11	206	84-1507
Lifetime (3186 days)	3107	0.98	34.08	27	3-100	618.34	482	9-11100	502.84	125	2-31585

Subtyping

SCUEAL usage summary as of Fri Feb 22 00:01:03 2019 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 6006 6006.00 82.91 4 0-500

Last 7 days 6006 858.00 82.91 4 0-500

Last 30 days 6006 200.20 82.91 4 0-500

Lifetime (3521 days) 7310 2.08 88.07 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	6006	6006.00	82.91	4	0-500
Last 7 days	6006	858.00	82.91	4	0-500
Last 30 days	6006	200.20	82.91	4	0-500
Lifetime (3521 days)	7310	2.08	88.07	5	0-500

Top 10 Subtypes (out of 643769 sequences)

Subtypes Times found % found

B 252038 39.2

C 109188 17.0

G 45646 7.1

A1 40635 6.3

Complex 26819 4.2

AE 18955 2.9

D 18642 2.9

CRF14 11733 1.8

F1 10111 1.6

B,C recombinant 8360 1.3

Subtypes	Times found	% found
B	252038	39.2
C	109188	17.0
G	45646	7.1
A1	40635	6.3
Complex	26819	4.2
AE	18955	2.9
D	18642	2.9
CRF14	11733	1.8
F1	10111	1.6
B,C recombinant	8360	1.3

Coevolution

BGM usage summary as of Fri Feb 22 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 1 1.00 11 11 11-11 1 1 1-1 4 4 4-4

Last 7 days 1 0.14 11 11 11-11 1 1 1-1 4 4 4-4

Last 30 days 33 1.10 99.30 112 3-415 1.28 0.27 0.16- 16.90 532.67 63 1-8123

Lifetime (2115 days) 8879 4.20 65.11 30 0-1033 2.25 0.98 0.01-263 2867.12 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	1	1.00	11	11	11-11	1	1	1-1	4	4	4-4
Last 7 days	1	0.14	11	11	11-11	1	1	1-1	4	4	4-4
Last 30 days	33	1.10	99.30	112	3-415	1.28	0.27	0.16- 16.90	532.67	63	1-8123
Lifetime (2115 days)	8879	4.20	65.11	30	0-1033	2.25	0.98	0.01-263	2867.12	93	0-2900666

UCSD Viral Evolution Group 2004-2019