Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Wed Mar 10 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 41 41.00 24.68 16 8-148 370.02 275 53-1921 16.63 10.68 3.35- 79.84

Last 7 days 182 26.00 25.92 15.50 4-163 404 320.50 53-2978 17.75 11.16 1.60- 192.10

Last 30 days 721 24.03 31.88 22 3-245 418.81 263 15-3965 33.51 8.62 0.95- 2938.17

Lifetime (2245 days) 13922 6.20 30.99 19 3-247 348.07 232 2-9794 35.82 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	41	41.00	24.68	16	8-148	370.02	275	53-1921	16.63	10.68	3.35- 79.84
Last 7 days	182	26.00	25.92	15.50	4-163	404	320.50	53-2978	17.75	11.16	1.60- 192.10
Last 30 days	721	24.03	31.88	22	3-245	418.81	263	15-3965	33.51	8.62	0.95- 2938.17
Lifetime (2245 days)	13922	6.20	30.99	19	3-247	348.07	232	2-9794	35.82	15.29	0.95-4721

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 7569 54.4
REV 1687 12.1
010000 1589 11.4
F81 465 3.3
TRN93 402 2.9
012212 215 1.5
001101 149 1.1
012012 122 0.9
000010 110 0.8
010232 90 0.6

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 12.1 10857 78.0
0.05 1.0 7.5 2383 17.1
0.25 1.2 36.1 198 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 0.6
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 Wed Mar 10 00:00:10 2010 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 19 19.00 28.95 22 6-78 321.74 249 108-886 58.32 38 3-197

Last 7 days 157 22.43 41.39 26 4-196 415.99 366 63-2472 75.33 33 1-838

Last 30 days 633 21.10 30.75 21 3-197 416.44 248 15-3965 63.47 22 1-2778

Lifetime (1896 days) 18053 9.52 29.32 21 3-200 394.11 262 4-9528 139.18 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	19	19.00	28.95	22	6-78	321.74	249	108-886	58.32	38	3-197
Last 7 days	157	22.43	41.39	26	4-196	415.99	366	63-2472	75.33	33	1-838
Last 30 days	633	21.10	30.75	21	3-197	416.44	248	15-3965	63.47	22	1-2778
Lifetime (1896 days)	18053	9.52	29.32	21	3-200	394.11	262	4-9528	139.18	45	0-10979

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 7236 40.1
REV 2947 16.3
010000 2259 12.5
F81 742 4.1
TRN93 709 3.9
012212 325 1.8
000010 251 1.4
001101 227 1.3
010232 216 1.2
012012 204 1.1

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 20.4 14762 81.8
0.05 0.9 14.6 2475 13.7
0.2 2.1 15.5 280 1.6
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 Wed Mar 10 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 16 16.00 23.44 23 6-50 322 262 108-886 265.75 284.50 36-495

Last 7 days 113 16.14 21.86 19 4-62 370.47 316 72-2472 214.12 110 12-3110

Last 30 days 522 17.40 16.52 11.50 3-74 401.22 263 15-3965 313.44 101 1-21574

Lifetime (1896 days) 10663 5.62 16.28 14 2-110 420.49 267 4-9528 475.44 241 0-37794

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	16	16.00	23.44	23	6-50	322	262	108-886	265.75	284.50	36-495
Last 7 days	113	16.14	21.86	19	4-62	370.47	316	72-2472	214.12	110	12-3110
Last 30 days	522	17.40	16.52	11.50	3-74	401.22	263	15-3965	313.44	101	1-21574
Lifetime (1896 days)	10663	5.62	16.28	14	2-110	420.49	267	4-9528	475.44	241	0-37794

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 4691 44.0
010000 1521 14.3
REV 1279 12.0
F81 471 4.4
TRN93 459 4.3
012012 176 1.7
012212 153 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 8893 83.4
10 5.9 34.1 408 3.8
90 30.5 3.7 400 3.8
100 2.9 22.2 337 3.2
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 0.2

Model Selection

ModelSelection usage summary as of Wed Mar 10 00:00:29 2010 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 31 31.00 20.42 22 6-78 625.32 317 53-1969

Last 7 days 137 19.57 20.36 14 4-78 573.82 323 53-3184

Last 30 days 645 21.50 28.47 16 3-241 437.11 244 15-3965

Lifetime (953 days) 10794 11.33 29.76 19 3-250 445.74 268 4-10000

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	31	31.00	20.42	22	6-78	625.32	317	53-1969
Last 7 days	137	19.57	20.36	14	4-78	573.82	323	53-3184
Last 30 days	645	21.50	28.47	16	3-241	437.11	244	15-3965
Lifetime (953 days)	10794	11.33	29.76	19	3-250	445.74	268	4-10000

Top 10 Models

Model Times selected % selected

HKY85 3408 31.6
F81 1023 9.5
TRN93 654 6.1
012212 447 4.1
010232 338 3.1
012232 283 2.6
012012 278 2.6
000010 276 2.6
001101 270 2.5
010230 245 2.3

Model	Times selected	% selected
HKY85	3408	31.6
F81	1023	9.5
TRN93	654	6.1
012212	447	4.1
010232	338	3.1
012232	283	2.6
012012	278	2.6
000010	276	2.6
001101	270	2.5
010230	245	2.3

Protein Model Selection

ModelSelectionP usage summary as of Wed Mar 10 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 (645 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 (645 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 Wed Mar 10 00:00:35 2010 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 28 28.00 22.79 18 6-98 1069 1053 324-3198 560.93 99 1-3029

Last 7 days 89 12.71 25.62 16 3-98 1957.98 1116 216-9981 775.33 253 1-3774

Last 30 days 544 18.13 23.70 18 3-100 1369.54 1095 60-9981 968.17 222 1-3939

Lifetime (1197 days) 9467 7.91 18.89 15 2-100 2180.73 1146 57-46625 1051.58 289 1-55555

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	28	28.00	22.79	18	6-98	1069	1053	324-3198	560.93	99	1-3029
Last 7 days	89	12.71	25.62	16	3-98	1957.98	1116	216-9981	775.33	253	1-3774
Last 30 days	544	18.13	23.70	18	3-100	1369.54	1095	60-9981	968.17	222	1-3939
Lifetime (1197 days)	9467	7.91	18.89	15	2-100	2180.73	1146	57-46625	1051.58	289	1-55555

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	3623	38.3
HKY85	2995	31.6
010000	430	4.5
REV	415	4.4
TRN93	279	2.9
F81	260	2.7
010232	113	1.2
012212	109	1.2
010230	91	1.0
012232	72	0.8

delta AIC range	Times found	% found
0-10	2797	29.5
10-20	439	4.6
20-30	372	3.9
30-40	326	3.4
40-50	278	2.9
50-60	257	2.7
60-70	199	2.1
70-80	157	1.7
80-90	157	1.7
90-100	124	1.3
> 100	4361	46.1

Number of breakpoints	Times found	% found
0	2165	22.9
1	2277	24.1
2	1674	17.7
3	1051	11.1
4	661	7.0
5	462	4.9
6	307	3.2
7	215	2.3
8	133	1.4
9	126	1.3
≥ 10	396	4.2

SBP

SBP usage summary as of Wed Mar 10 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 11 11.00 40 10 6-120 6.18 1 1-46 231.91 16 4-1220

Last 7 days 38 5.43 49.13 22.50 6-250 7.95 3 1-46 370.84 24.50 1-6041

Last 30 days 158 5.27 36.80 16 5-250 6.03 1 1-62 148.83 14 0-6041

Lifetime (1402 days) 4413 3.15 26.04 19 2-250 30.03 1 1-45015 241.40 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	11	11.00	40	10	6-120	6.18	1	1-46	231.91	16	4-1220
Last 7 days	38	5.43	49.13	22.50	6-250	7.95	3	1-46	370.84	24.50	1-6041
Last 30 days	158	5.27	36.80	16	5-250	6.03	1	1-62	148.83	14	0-6041
Lifetime (1402 days)	4413	3.15	26.04	19	2-250	30.03	1	1-45015	241.40	28	0-129312

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	2117	48.0
REV	515	11.7
010000	316	7.2
F81	241	5.5
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	1710	38.7
10-20	219	5.0
20-30	196	4.4
30-40	139	3.1
40-50	128	2.9
50-60	92	2.1
60-70	78	1.8
70-80	76	1.7
80-90	56	1.3
90-100	56	1.3
> 100	1663	37.7

PARRIS

PARRIS usage summary as of Wed Mar 10 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 2 2.00 18.50 18.50 9-28 408 408 211-605 69 69 48-90

Last 7 days 41 5.86 20.83 15 5-62 294.17 265 72-947 303.20 90 10-3981

Last 30 days 146 4.87 16.66 11 3-74 394.29 342.50 27-1717 242.55 83 3-4667

Lifetime (952 days) 2551 2.68 17.53 16 3-74 429.04 300 11-6061 436.87 205 1-10666

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	18.50	18.50	9-28	408	408	211-605	69	69	48-90
Last 7 days	41	5.86	20.83	15	5-62	294.17	265	72-947	303.20	90	10-3981
Last 30 days	146	4.87	16.66	11	3-74	394.29	342.50	27-1717	242.55	83	3-4667
Lifetime (952 days)	2551	2.68	17.53	16	3-74	429.04	300	11-6061	436.87	205	1-10666

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	1238	48.5
010000	256	10.0
REV	215	8.4
F81	129	5.1
TRN93	115	4.5
012212	65	2.5
012012	44	1.7
012030	32	1.3
012232	30	1.2
000010	25	1.0

p-values range	Times found	% found
0-0.1	474	18.6
0.1-0.2	96	3.8
0.2-0.3	102	4.0
0.3-0.4	57	2.2
0.4-0.5	80	3.1
0.5-0.6	63	2.5
0.6-0.7	53	2.1
0.7-0.8	75	2.9
0.8-0.9	73	2.9
0.9-1	1478	57.9

GA Branch

GABranch usage summary as of Wed Mar 10 00:00:47 2010 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 24.50 24 22-28 210.75 230 108-275 4161.25 4405.50 2818-5016

Last 7 days 31 4.43 15.03 14 4-30 323.90 297 63-1288 2973 2111 5-12074

Last 30 days 161 5.37 13.30 11 4-30 366.34 327 57-1288 4001.43 1320 5-33721

Lifetime (945 days) 2653 2.81 14.60 14 3-30 485.32 283 14-10000 6378.86 2110 2-253122

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	24.50	24	22-28	210.75	230	108-275	4161.25	4405.50	2818-5016
Last 7 days	31	4.43	15.03	14	4-30	323.90	297	63-1288	2973	2111	5-12074
Last 30 days	161	5.37	13.30	11	4-30	366.34	327	57-1288	4001.43	1320	5-33721
Lifetime (945 days)	2653	2.81	14.60	14	3-30	485.32	283	14-10000	6378.86	2110	2-253122

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	1242	46.8
REV	331	12.5
010000	321	12.1
F81	86	3.2
TRN93	83	3.1
012012	44	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	0.2
2	912	34.4
3	958	36.1
4	519	19.6
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 Wed Mar 10 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 9 9.00 33.33 26 10-119 2.42 1.75 1.11- 6.50 197.78 84 24-675

Last 7 days 41 5.86 48.78 26 7-237 1.69 1.13 0.13- 6.71 183.80 96 1-675

Last 30 days 93 3.10 60.40 28 6-354 1.19 0.83 0.09- 6.71 252.12 60 0-4383

Lifetime (726 days) 1768 2.44 53.75 31.50 1-482 2.20 0.97 0.02- 58.76 2235.00 209.50 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	9	9.00	33.33	26	10-119	2.42	1.75	1.11- 6.50	197.78	84	24-675
Last 7 days	41	5.86	48.78	26	7-237	1.69	1.13	0.13- 6.71	183.80	96	1-675
Last 30 days	93	3.10	60.40	28	6-354	1.19	0.83	0.09- 6.71	252.12	60	0-4383
Lifetime (726 days)	1768	2.44	53.75	31.50	1-482	2.20	0.97	0.02- 58.76	2235.00	209.50	0-1103550

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