Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Mon Mar 15 00:00:01 2010 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 40.80 22 13-74 309.40 300 86-566 16.92 10.94 3.25- 30.03

Last 7 days 175 25.00 30.29 20 5-148 390.81 316 53-2451 21.87 11.92 3.25- 192.10

Last 30 days 669 22.30 32.31 23 3-245 397.90 288 20-3434 36.06 10.65 0.95- 2938.17

Lifetime (2250 days) 14026 6.23 30.99 19 3-247 348.23 232 2-9794 35.71 15.29 0.95-4721

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	40.80	22	13-74	309.40	300	86-566	16.92	10.94	3.25- 30.03
Last 7 days	175	25.00	30.29	20	5-148	390.81	316	53-2451	21.87	11.92	3.25- 192.10
Last 30 days	669	22.30	32.31	23	3-245	397.90	288	20-3434	36.06	10.65	0.95- 2938.17
Lifetime (2250 days)	14026	6.23	30.99	19	3-247	348.23	232	2-9794	35.71	15.29	0.95-4721

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 7616 54.3
REV 1692 12.1
010000 1600 11.4
F81 467 3.3
TRN93 410 2.9
012212 216 1.5
001101 149 1.1
012012 139 1.0
000010 110 0.8
010232 90 0.6

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 12.1 10958 78.1
0.05 1.0 7.5 2384 17.0
0.25 1.2 36.2 200 1.4
0.2 1.0 27.8 140 1.0
0.5 5.5 27.8 98 0.7
0.3 1.2 26.1 77 0.5
0.01 1.1 6.6 62 0.4
0.9 23.6 53.2 30 0.2
0.15 2.5 32.4 17 0.1
0.06 0.3 6.2 10 0.1

FEL

FEL usage summary as of Mon Mar 15 00:00:11 2010 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 7 7.00 49.86 50 22-91 132.29 89 82-300 44.71 33 7-108

Last 7 days 154 22.00 33.34 22 6-140 445.03 366 72-2451 85.02 35 3-1121

Last 30 days 557 18.57 34.39 22 4-197 383.82 267 27-3434 76.76 28 1-2778

Lifetime (1901 days) 18165 9.56 29.35 21 3-200 394.31 263 4-9528 138.83 45 0-10979

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	7	7.00	49.86	50	22-91	132.29	89	82-300	44.71	33	7-108
Last 7 days	154	22.00	33.34	22	6-140	445.03	366	72-2451	85.02	35	3-1121
Last 30 days	557	18.57	34.39	22	4-197	383.82	267	27-3434	76.76	28	1-2778
Lifetime (1901 days)	18165	9.56	29.35	21	3-200	394.31	263	4-9528	138.83	45	0-10979

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 7286 40.1
REV 2959 16.3
010000 2278 12.5
F81 746 4.1
TRN93 711 3.9
012212 326 1.8
000010 251 1.4
001101 227 1.2
012012 217 1.2
010232 216 1.2

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 20.3 14874 81.9
0.05 0.9 14.6 2475 13.6
0.2 2.1 15.5 280 1.5
0.25 3.1 35.5 231 1.3
0.5 5.2 39.7 70 0.4
0.01 0.4 17.9 67 0.4
0.15 1.4 15.0 42 0.2
0.19 0.2 4.5 14 0.1
0.3 1.9 11.9 12 0.1
0.06 0.8 10.6 11 0.1

REL

REL usage summary as of Mon Mar 15 00:00:23 2010 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 22 22 22-22 86 86 86-86 49 49 49-49

Last 7 days 71 10.14 22.75 22 5-66 435.46 328 72-2451 508.82 272 20-5101

Last 30 days 464 15.47 17.70 12 3-74 356.80 260 20-3333 342.08 110 1-21574

Lifetime (1901 days) 10713 5.64 16.31 14 2-110 420.44 267 4-9528 475.99 241 0-37794

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	22	22	22-22	86	86	86-86	49	49	49-49
Last 7 days	71	10.14	22.75	22	5-66	435.46	328	72-2451	508.82	272	20-5101
Last 30 days	464	15.47	17.70	12	3-74	356.80	260	20-3333	342.08	110	1-21574
Lifetime (1901 days)	10713	5.64	16.31	14	2-110	420.44	267	4-9528	475.99	241	0-37794

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 4715 44.0
010000 1530 14.3
REV 1281 12.0
F81 471 4.4
TRN93 463 4.3
012012 178 1.7
012212 154 1.4
001101 132 1.2
010232 110 1.0
000010 102 1.0

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

50 4.0 22.6 8943 83.5
10 5.9 34.1 408 3.8
90 30.5 3.7 400 3.7
100 2.9 22.2 337 3.1
20 9.6 34.0 325 3.0
95 3.1 21.6 96 0.9
40 6.7 15.5 50 0.5
0.1 53.1 84.3 47 0.4
30 2.9 25.3 33 0.3
5 12.3 21.9 16 0.1

Model Selection

ModelSelection usage summary as of Mon Mar 15 00:00:30 2010 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 9 9.00 36.78 22 9-91 159.89 86 63-566

Last 7 days 175 25.00 26.74 21 4-116 444.83 301 53-2518

Last 30 days 639 21.30 27.13 16 3-214 422.18 221 20-3434

Lifetime (958 days) 10908 11.39 29.77 19 3-250 444.83 268.67 4-10000

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	9	9.00	36.78	22	9-91	159.89	86	63-566
Last 7 days	175	25.00	26.74	21	4-116	444.83	301	53-2518
Last 30 days	639	21.30	27.13	16	3-214	422.18	221	20-3434
Lifetime (958 days)	10908	11.39	29.77	19	3-250	444.83	268.67	4-10000

Top 10 Models

Model Times selected % selected

HKY85 3448 31.6
F81 1033 9.5
TRN93 666 6.1
012212 448 4.1
010232 338 3.1
012012 299 2.7
012232 283 2.6
000010 276 2.5
001101 270 2.5
010230 245 2.2

Model	Times selected	% selected
HKY85	3448	31.6
F81	1033	9.5
TRN93	666	6.1
012212	448	4.1
010232	338	3.1
012012	299	2.7
012232	283	2.6
000010	276	2.5
001101	270	2.5
010230	245	2.2

Protein Model Selection

ModelSelectionP usage summary as of Mon Mar 15 00:00:35 2010 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 56 56 56-56 60 60 60-60

Last 30 days 11 0.37 71.73 48 5-244 1441 173 60-6578

Lifetime (650 days) 291 0.45 38.57 24 2-244 680.42 412 35-18120

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	1	0.14	56	56	56-56	60	60	60-60
Last 30 days	11	0.37	71.73	48	5-244	1441	173	60-6578
Lifetime (650 days)	291	0.45	38.57	24	2-244	680.42	412	35-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton) 71 24.4
WAG (Whelan and Goldman) 53 18.2
LG (Le and Gascuel) 48 16.5
HIV (between hosts) 39 13.4
BLOSUM62 26 8.9
HIV (within host) 19 6.5
Dayhoff 10 3.4
IAV (Influenza A virus) 8 2.7
VT (Vingron and Muller) 6 2.1
rtREV (reverse transcriptase) 5 1.7

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)	71	24.4
WAG (Whelan and Goldman)	53	18.2
LG (Le and Gascuel)	48	16.5
HIV (between hosts)	39	13.4
BLOSUM62	26	8.9
HIV (within host)	19	6.5
Dayhoff	10	3.4
IAV (Influenza A virus)	8	2.7
VT (Vingron and Muller)	6	2.1
rtREV (reverse transcriptase)	5	1.7

GARD

GARD usage summary as of Mon Mar 15 00:00:36 2010 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 14 14.00 13 10 4-50 482.57 307.50 189-1020 71.64 9 1-496

Last 7 days 108 15.43 21.19 18 3-98 1093.71 989 189-9981 706.23 106 1-3774

Last 30 days 527 17.57 22.32 18 3-100 1293.75 1020 60-9981 886.38 184 1-3939

Lifetime (1202 days) 9540 7.94 18.90 15 2-100 2171.49 1137 57-46625 1049.31 287 1-55555

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	14	14.00	13	10	4-50	482.57	307.50	189-1020	71.64	9	1-496
Last 7 days	108	15.43	21.19	18	3-98	1093.71	989	189-9981	706.23	106	1-3774
Last 30 days	527	17.57	22.32	18	3-100	1293.75	1020	60-9981	886.38	184	1-3939
Lifetime (1202 days)	9540	7.94	18.90	15	2-100	2171.49	1137	57-46625	1049.31	287	1-55555

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	3696	38.7
HKY85	2995	31.4
010000	430	4.5
REV	415	4.4
TRN93	279	2.9
F81	260	2.7
010232	113	1.2
012212	109	1.1
010230	91	1.0
012232	72	0.8

delta AIC range	Times found	% found
0-10	2828	29.6
10-20	439	4.6
20-30	373	3.9
30-40	327	3.4
40-50	280	2.9
50-60	258	2.7
60-70	200	2.1
70-80	158	1.7
80-90	161	1.7
90-100	124	1.3
> 100	4392	46.0

Number of breakpoints	Times found	% found
0	2195	23.0
1	2285	24.0
2	1682	17.6
3	1054	11.0
4	667	7.0
5	469	4.9
6	315	3.3
7	216	2.3
8	134	1.4
9	127	1.3
≥ 10	396	4.2

SBP

SBP usage summary as of Mon Mar 15 00:00:42 2010 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 7 7.00 14 4 4-74 10.71 11 1-27 77.43 0 0-537

Last 7 days 48 6.86 32.27 13 4-250 6.44 1 1-58 239.48 9 0-6041

Last 30 days 148 4.93 33.41 15 4-250 6.38 1 1-58 156.84 10 0-6041

Lifetime (1407 days) 4448 3.16 26.03 19 2-250 29.85 1 1-45015 240.15 28 0-129312

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	7	7.00	14	4	4-74	10.71	11	1-27	77.43	0	0-537
Last 7 days	48	6.86	32.27	13	4-250	6.44	1	1-58	239.48	9	0-6041
Last 30 days	148	4.93	33.41	15	4-250	6.38	1	1-58	156.84	10	0-6041
Lifetime (1407 days)	4448	3.16	26.03	19	2-250	29.85	1	1-45015	240.15	28	0-129312

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	2133	48.0
REV	519	11.7
010000	319	7.2
F81	241	5.4
TRN93	209	4.7
010232	115	2.6
012212	62	1.4
012232	56	1.3
000010	50	1.1
010212	47	1.1

IC improvement range	Times found	% found
0-10	1729	38.9
10-20	219	4.9
20-30	196	4.4
30-40	139	3.1
40-50	129	2.9
50-60	92	2.1
60-70	78	1.8
70-80	77	1.7
80-90	58	1.3
90-100	56	1.3
> 100	1675	37.7

PARRIS

PARRIS usage summary as of Mon Mar 15 00:00:46 2010 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 9 9.00 8 4 4-22 123.44 86 63-260 25.78 13 4-87

Last 7 days 75 10.71 17.49 13 4-75 215.24 89 63-947 285.13 130 4-2202

Last 30 days 198 6.60 17.38 12 4-75 303.59 197.50 27-1022 257.24 98 3-4667

Lifetime (957 days) 2622 2.74 17.53 15.50 3-75 422.54 293 11-6061 432.21 204 1-10666

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	9	9.00	8	4	4-22	123.44	86	63-260	25.78	13	4-87
Last 7 days	75	10.71	17.49	13	4-75	215.24	89	63-947	285.13	130	4-2202
Last 30 days	198	6.60	17.38	12	4-75	303.59	197.50	27-1022	257.24	98	3-4667
Lifetime (957 days)	2622	2.74	17.53	15.50	3-75	422.54	293	11-6061	432.21	204	1-10666

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	1254	47.8
010000	258	9.8
REV	221	8.4
F81	165	6.3
TRN93	115	4.4
012212	65	2.5
012012	45	1.7
012030	32	1.2
012232	30	1.1
000010	25	1.0

p-values range	Times found	% found
0-0.1	501	19.1
0.1-0.2	103	3.9
0.2-0.3	107	4.1
0.3-0.4	60	2.3
0.4-0.5	86	3.3
0.5-0.6	65	2.5
0.6-0.7	55	2.1
0.7-0.8	75	2.9
0.8-0.9	77	2.9
0.9-1	1493	56.9

GA Branch

GABranch usage summary as of Mon Mar 15 00:00:48 2010 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 10 10.00 6.90 4 4-22 278.30 155.50 78-1359 503.50 16 8-2188

Last 7 days 33 4.71 12.55 10 4-28 366.39 260 78-1359 2983.33 1395 8-18339

Last 30 days 154 5.13 12.82 9 4-30 352.21 312.50 57-1359 3767.29 1220 5-33721

Lifetime (950 days) 2676 2.82 14.56 14 3-30 484.03 283 14-10000 6345.98 2089 2-253122

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	10	10.00	6.90	4	4-22	278.30	155.50	78-1359	503.50	16	8-2188
Last 7 days	33	4.71	12.55	10	4-28	366.39	260	78-1359	2983.33	1395	8-18339
Last 30 days	154	5.13	12.82	9	4-30	352.21	312.50	57-1359	3767.29	1220	5-33721
Lifetime (950 days)	2676	2.82	14.56	14	3-30	484.03	283	14-10000	6345.98	2089	2-253122

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	1249	46.7
REV	336	12.6
010000	324	12.1
F81	86	3.2
TRN93	83	3.1
012012	45	1.7
012232	34	1.3
000010	31	1.2
001101	27	1.0
012032	26	1.0

the number of dN/dS classes range	Times found	% found
1	4	0.1
2	921	34.4
3	969	36.2
4	522	19.5
5	163	6.1
6	62	2.3
7	26	1.0
8	9	0.3
9	0	0.0

Co-evolution

BGM usage summary as of Mon Mar 15 00:00:49 2010 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 15 2.14 35.67 29 10-119 1.78 1.38 0.16- 6.50 193.93 60 1-910

Last 30 days 89 2.97 58.40 29 6-354 1.13 0.58 0.11- 6.71 194.72 50 0-1194

Lifetime (731 days) 1772 2.42 53.74 32 1-482 2.20 0.97 0.02- 58.76 2230.58 209 0-1103550

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	15	2.14	35.67	29	10-119	1.78	1.38	0.16- 6.50	193.93	60	1-910
Last 30 days	89	2.97	58.40	29	6-354	1.13	0.58	0.11- 6.71	194.72	50	0-1194
Lifetime (731 days)	1772	2.42	53.74	32	1-482	2.20	0.97	0.02- 58.76	2230.58	209	0-1103550

Sergei L. Kosakovsky Pond, Art Poon, Wayne Delport and Simon D.W. Frost, 2004-2010