Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Sun Apr 22 00:00:03 2018 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 12 9 6-21 121.67 75 62-228 0.80 0.60 0.53- 1.28

Last 7 days 223 31.86 51.09 27 3-402 464.80 326 35-2334 10.24 3.78 0.22- 161.09

Last 30 days 798 26.60 51.97 35 3-421 484.06 325 19-4249 11.72 4.54 0.22- 265.82

Lifetime (2709 days) 86970 32.10 51.99 25 3-684 487.37 325 1-11903 21.56 6.24 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	3	3.00	12	9	6-21	121.67	75	62-228	0.80	0.60	0.53- 1.28
Last 7 days	223	31.86	51.09	27	3-402	464.80	326	35-2334	10.24	3.78	0.22- 161.09
Last 30 days	798	26.60	51.97	35	3-421	484.06	325	19-4249	11.72	4.54	0.22- 265.82
Lifetime (2709 days)	86970	32.10	51.99	25	3-684	487.37	325	1-11903	21.56	6.24	0.16- 7571.98

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 45044 51.8
TRN93 12804 14.7
REV 9261 10.6
F81 3836 4.4
010230 985 1.1
010232 976 1.1
012212 920 1.1
012012 841 1.0
012232 743 0.9
010000 660 0.8

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 0.6 16.2 72903 83.8
0.05 0.5 14.5 10581 12.2
0.2 0.9 17.3 1251 1.4
0.25 2.3 25.7 723 0.8
0.5 4.4 55.2 561 0.6
0.01 0.8 9.4 521 0.6
0.15 2.9 14.8 88 0.1
0.0024 0.0 2.3 45 0.1
0.3 0.2 20.0 45 0.1
0.0048 0.0 0.5 33 0.0

FEL

FEL usage summary as of Sun Apr 22 00:00:15 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 13.50 13.50 6-21 68.50 68.50 62-75 9 9 5-13

Last 7 days 97 13.86 38.13 21 4-369 381.74 309 51-2334 51.99 33 5-433

Last 30 days 578 19.27 33.45 14 3-377 500.76 273 19-3801 68.15 26 1-3013

Lifetime (1809 days) 97403 53.84 44.21 24 3-787 478.62 325 1-11276 141.06 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	2	2.00	13.50	13.50	6-21	68.50	68.50	62-75	9	9	5-13
Last 7 days	97	13.86	38.13	21	4-369	381.74	309	51-2334	51.99	33	5-433
Last 30 days	578	19.27	33.45	14	3-377	500.76	273	19-3801	68.15	26	1-3013
Lifetime (1809 days)	97403	53.84	44.21	24	3-787	478.62	325	1-11276	141.06	44	0-26278

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 43870 45.0
REV 12874 13.2
TRN93 9551 9.8
F81 4792 4.9
010000 3917 4.0
010232 2021 2.1
012012 1402 1.4
012212 1305 1.3
010230 1189 1.2
012032 926 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 24.2 78942 81.0
0.05 0.9 19.3 14468 14.9
0.2 2.2 29.1 1877 1.9
0.25 3.2 33.4 845 0.9
0.01 0.4 14.3 484 0.5
0.5 5.6 44.7 187 0.2
0.15 2.9 21.9 131 0.1
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 Sun Apr 22 00:00:28 2018 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 11 6 6-21 70.67 75 62-75 50.33 38 37-76

Last 7 days 37 5.29 15.30 12 5-53 546.05 291 51-2334 341.35 90 8-6351

Last 30 days 296 9.87 25.35 15 4-75 494.08 247 19-3801 327.36 88.50 2-11181

Lifetime (1808 days) 54380 30.08 20.60 16 2-110 481.00 318 1-10798 363.05 108 0-39109

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	3	3.00	11	6	6-21	70.67	75	62-75	50.33	38	37-76
Last 7 days	37	5.29	15.30	12	5-53	546.05	291	51-2334	341.35	90	8-6351
Last 30 days	296	9.87	25.35	15	4-75	494.08	247	19-3801	327.36	88.50	2-11181
Lifetime (1808 days)	54380	30.08	20.60	16	2-110	481.00	318	1-10798	363.05	108	0-39109

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 28809 53.0
REV 5573 10.2
TRN93 3163 5.8
F81 3098 5.7
010000 2329 4.3
012012 1040 1.9
001101 714 1.3
010232 683 1.3
012212 659 1.2
012032 554 1.0

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

50 4.3 27.7 49105 90.3
100 4.2 22.6 1283 2.4
90 19.4 11.1 890 1.6
20 7.3 36.2 807 1.5
10 5.8 31.9 728 1.3
95 2.3 28.0 642 1.2
40 2.5 24.5 144 0.3
80 3.1 28.0 103 0.2
30 10.2 20.6 89 0.2
25 2.5 38.2 79 0.1

TOGGLE

Toggle usage summary as of Sun Apr 22 00:00:34 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 16 16 16-16 326 326 326-326 604 604 431-777

Last 30 days 3 0.10 14.67 16 12-16 880.33 326 326-1989 689.67 777 431-861

Lifetime (2889 days) 1040 0.36 48.36 39 7-150 570.62 346 16-3789 3832.52 2012.50 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	2	0.29	16	16	16-16	326	326	326-326	604	604	431-777
Last 30 days	3	0.10	14.67	16	12-16	880.33	326	326-1989	689.67	777	431-861
Lifetime (2889 days)	1040	0.36	48.36	39	7-150	570.62	346	16-3789	3832.52	2012.50	31-42841

Model Select.

ModelSelection usage summary as of Sun Apr 22 00:00:35 2018 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 3 3.00 112.67 164 9-165 426.33 525 228-526

Last 7 days 196 28.00 58.57 35 3-428 390.83 309 51-2334

Last 30 days 766 25.53 49.45 26 3-428 524.50 359 19-3800

Lifetime (1809 days) 94493 52.23 41.55 22 3-656 515.40 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	3	3.00	112.67	164	9-165	426.33	525	228-526
Last 7 days	196	28.00	58.57	35	3-428	390.83	309	51-2334
Last 30 days	766	25.53	49.45	26	3-428	524.50	359	19-3800
Lifetime (1809 days)	94493	52.23	41.55	22	3-656	515.40	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 22713 24.0
TRN93 12401 13.1
F81 8324 8.8
010232 4182 4.4
012012 3077 3.3
012212 2796 3.0
010230 2236 2.4
012032 2159 2.3
012232 2116 2.2
001101 1986 2.1

Model	Times selected	% selected
HKY85	22713	24.0
TRN93	12401	13.1
F81	8324	8.8
010232	4182	4.4
012012	3077	3.3
012212	2796	3.0
010230	2236	2.4
012032	2159	2.3
012232	2116	2.2
001101	1986	2.1

Protein Model Select.

ModelSelectionP usage summary as of Sun Apr 22 00:00:44 2018 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 1 1.00 8 8 8-8 228 228 228-228

Last 7 days 2 0.29 217 217 8-426 334 334 228-440

Last 30 days 10 0.33 124.10 87.50 8-426 1301.70 643 228-3551

Lifetime (3610 days) 3726 1.03 45.76 25 2-499 646.42 444 3-18120

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	1	1.00	8	8	8-8	228	228	228-228
Last 7 days	2	0.29	217	217	8-426	334	334	228-440
Last 30 days	10	0.33	124.10	87.50	8-426	1301.70	643	228-3551
Lifetime (3610 days)	3726	1.03	45.76	25	2-499	646.42	444	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 547 14.7
JTT (Jones,Taylor,Thornton) 399 10.7
BLOSUM62+F 310 8.3
WAG (Whelan and Goldman)+F 307 8.2
WAG (Whelan and Goldman) 240 6.4
IAV (Influenza A virus)+F 235 6.3
HIV (within host)+F 230 6.2
IAV (Influenza A virus) 215 5.8
BLOSUM62 163 4.4
LG (Le and Gascuel) 149 4.0

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)+F	547	14.7
JTT (Jones,Taylor,Thornton)	399	10.7
BLOSUM62+F	310	8.3
WAG (Whelan and Goldman)+F	307	8.2
WAG (Whelan and Goldman)	240	6.4
IAV (Influenza A virus)+F	235	6.3
HIV (within host)+F	230	6.2
IAV (Influenza A virus)	215	5.8
BLOSUM62	163	4.4
LG (Le and Gascuel)	149	4.0

GARD

GARD usage summary as of Sun Apr 22 00:00:46 2018 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 1 1.00 164 164 164-164 1575 1575 1575-1575 2433 2433 2433-2433

Last 7 days 44 6.29 31.77 15 3-211 1631.68 1773 210-3450 1579.73 828.50 68-3954

Last 30 days 177 5.90 31.34 17 3-211 1955.79 1185 156-10653 1321.30 576 36-4731

Lifetime (4162 days) 73591 17.68 26.82 18 2-300 2030.66 1112 20-46625 1270.38 374 1-272974

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	1	1.00	164	164	164-164	1575	1575	1575-1575	2433	2433	2433-2433
Last 7 days	44	6.29	31.77	15	3-211	1631.68	1773	210-3450	1579.73	828.50	68-3954
Last 30 days	177	5.90	31.34	17	3-211	1955.79	1185	156-10653	1321.30	576	36-4731
Lifetime (4162 days)	73591	17.68	26.82	18	2-300	2030.66	1112	20-46625	1270.38	374	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	61902	84.1
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	26685	36.3
10-20	2934	4.0
20-30	2359	3.2
30-40	2203	3.0
40-50	1808	2.5
50-60	1934	2.6
60-70	1395	1.9
70-80	1295	1.8
80-90	1192	1.6
90-100	1064	1.4
> 100	30722	41.7

Number of breakpoints	Times found	% found
0	22416	30.5
1	18652	25.3
2	11664	15.8
3	6761	9.2
4	4102	5.6
5	2841	3.9
6	1849	2.5
7	1400	1.9
8	932	1.3
9	759	1.0
≥ 10	2215	3.0

SBP

SBP usage summary as of Sun Apr 22 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 0

Last 7 days 12 1.71 102.25 53 10-377 7.75 2 1-54 294.08 67.50 1-1777

Last 30 days 53 1.77 66.96 37 6-500 127.49 3 1-1259 460.02 84 1-4406

Lifetime (1809 days) 20142 11.13 48.53 24 2-656 21.78 1 1-45015 473.32 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	12	1.71	102.25	53	10-377	7.75	2	1-54	294.08	67.50	1-1777
Last 30 days	53	1.77	66.96	37	6-500	127.49	3	1-1259	460.02	84	1-4406
Lifetime (1809 days)	20142	11.13	48.53	24	2-656	21.78	1	1-45015	473.32	41	0-279793

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	14442	71.7
REV	1311	6.5
010000	565	2.8
TRN93	500	2.5
F81	500	2.5
0123455	224	1.1
010232	215	1.1
012012	137	0.7
0112304567	114	0.6
010230	105	0.5

IC improvement range	Times found	% found
0-10	8697	43.2
10-20	886	4.4
20-30	763	3.8
30-40	617	3.1
40-50	501	2.5
50-60	401	2.0
60-70	350	1.7
70-80	368	1.8
80-90	278	1.4
90-100	300	1.5
> 100	6981	34.7

PARRIS

PARRIS usage summary as of Sun Apr 22 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 118 3.93 7.97 6 4-48 478.97 504 99-909 57.29 8 1-797

Lifetime (3917 days) 14142 3.61 20.19 15 3-75 484.22 328 7-11903 414.97 137 1-35284

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	0
Last 30 days	118	3.93	7.97	6	4-48	478.97	504	99-909	57.29	8	1-797
Lifetime (3917 days)	14142	3.61	20.19	15	3-75	484.22	328	7-11903	414.97	137	1-35284

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	7979	56.4
F81	1051	7.4
REV	995	7.0
TRN93	736	5.2
010000	429	3.0
012012	250	1.8
001101	166	1.2
012212	153	1.1
012032	127	0.9
010230	119	0.8

p-values range	Times found	% found
0-0.1	2597	18.4
0.1-0.2	502	3.5
0.2-0.3	456	3.2
0.3-0.4	359	2.5
0.4-0.5	325	2.3
0.5-0.6	386	2.7
0.6-0.7	363	2.6
0.7-0.8	349	2.5
0.8-0.9	344	2.4
0.9-1	8461	59.8

GA Branch

GABranch usage summary as of Sun Apr 22 00:01:00 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 3 0.43 10.33 9 5-17 1238.67 1150 232-2334 1740.67 1567 15-3640

Last 30 days 9 0.30 13.67 11 5-26 821.22 270 30-2334 1790.67 1567 15-6092

Lifetime (3910 days) 11566 2.96 13.73 12 3-30 514.75 329 9-11628 5302.42 1507 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	3	0.43	10.33	9	5-17	1238.67	1150	232-2334	1740.67	1567	15-3640
Last 30 days	9	0.30	13.67	11	5-26	821.22	270	30-2334	1790.67	1567	15-6092
Lifetime (3910 days)	11566	2.96	13.73	12	3-30	514.75	329	9-11628	5302.42	1507	1-636439

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8299	71.8
REV	613	5.3
010000	568	4.9
F81	414	3.6
TRN93	281	2.4
012012	131	1.1
001101	107	0.9
012212	64	0.6
010012	63	0.5
000010	60	0.5

the number of dN/dS classes range	Times found	% found
1	99	0.9
2	4239	36.7
3	3913	33.8
4	2163	18.7
5	756	6.5
6	227	2.0
7	111	1.0
8	35	0.3
9	23	0.2

CMS

CMS usage summary as of Sun Apr 22 00:01:02 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 1 0.14 41 41 41-41 511 511 511-511 19125 19125 19125-19125

Last 30 days 8 0.27 37 27.50 6-101 520.25 507.50 209-706 7405.12 2333 177-22833

Lifetime (3001 days) 3075 1.02 33.85 24 3-120 536.90 334 7-11276 17819.02 3918 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	1	0.14	41	41	41-41	511	511	511-511	19125	19125	19125-19125
Last 30 days	8	0.27	37	27.50	6-101	520.25	507.50	209-706	7405.12	2333	177-22833
Lifetime (3001 days)	3075	1.02	33.85	24	3-120	536.90	334	7-11276	17819.02	3918	59-2971964

Distribution of mBIC improvement

Number of inferred rate classes

mBIC improvement range	Times found	% found
0-10	183	6.0
10-20	141	4.6
20-30	186	6.0
30-40	212	6.9
40-50	239	7.8
50-60	173	5.6
60-70	170	5.5
70-80	126	4.1
80-90	168	5.5
90-100	107	3.5
> 100	1370	44.6

Number of rate classes	Times found	% found
1	0	0.0
2	1958	63.7
3	669	21.8
4	253	8.2
5	100	3.3
6	45	1.5
7	14	0.5
8	2	0.1
9	0	0.0
≥ 10	34	1.1

DEPS

DEPS usage summary as of Sun Apr 22 00:01:03 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 10 10 10-10 2334 2334 2334-2334 37 37 37-37

Lifetime (2880 days) 2716 0.94 32.00 24 3-100 580.16 435.50 9-11100 435.71 100 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	1	0.03	10	10	10-10	2334	2334	2334-2334	37	37	37-37
Lifetime (2880 days)	2716	0.94	32.00	24	3-100	580.16	435.50	9-11100	435.71	100	2-31585

Subtyping

SCUEAL usage summary as of Sun Apr 22 00:01:04 2018 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 5787 5787.00 82.34 4 0-500

Last 7 days 5787 826.71 82.34 4 0-500

Last 30 days 5787 192.90 82.34 4 0-500

Lifetime (3215 days) 7091 2.21 87.76 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	5787	5787.00	82.34	4	0-500
Last 7 days	5787	826.71	82.34	4	0-500
Last 30 days	5787	192.90	82.34	4	0-500
Lifetime (3215 days)	7091	2.21	87.76	5	0-500

Top 10 Subtypes (out of 622318 sequences)

Subtypes Times found % found

B 242050 38.9

C 107314 17.2

G 44715 7.2

A1 39575 6.4

Complex 25730 4.1

AE 17977 2.9

D 17101 2.7

CRF14 11644 1.9

F1 9752 1.6

B,C recombinant 8093 1.3

Subtypes	Times found	% found
B	242050	38.9
C	107314	17.2
G	44715	7.2
A1	39575	6.4
Complex	25730	4.1
AE	17977	2.9
D	17101	2.7
CRF14	11644	1.9
F1	9752	1.6
B,C recombinant	8093	1.3

Coevolution

BGM usage summary as of Sun Apr 22 00:01:06 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 4 0.57 72.75 49.50 6-186 0.78 0.53 0.05-2 62 2.50 1-242

Last 30 days 7 0.23 75.71 56 6-186 1.45 0.88 0.05- 4.93 681.43 6 1-4286

Lifetime (1809 days) 8697 4.81 64.75 30 0-1033 2.26 0.98 0.01-263 2917.15 96 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	4	0.57	72.75	49.50	6-186	0.78	0.53	0.05-2	62	2.50	1-242
Last 30 days	7	0.23	75.71	56	6-186	1.45	0.88	0.05- 4.93	681.43	6	1-4286
Lifetime (1809 days)	8697	4.81	64.75	30	0-1033	2.26	0.98	0.01-263	2917.15	96	0-2900666

UCSD Viral Evolution Group 2004-2018