Mercurial > repos > iuc > codeml
comparison test-data/1_run_codeml @ 0:961a712f9743 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
author | iuc |
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date | Tue, 29 Aug 2017 19:12:01 -0400 |
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-1:000000000000 | 0:961a712f9743 |
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1 CODONML (in paml version 4.9, March 2015) /tmp/tmpMdbfK7/files/000/dataset_1.dat | |
2 Model: One dN/dS ratio for branches, | |
3 Codon frequency model: F1x4 | |
4 ns = 6 ls = 13754 | |
5 | |
6 Codon usage in sequences | |
7 -------------------------------------------------------------------------------------------------------------------------------------- | |
8 Phe TTT 232 13 253 68 16 40 | Ser TCT 276 5 291 78 8 58 | Tyr TAT 98 3 95 29 3 27 | Cys TGT 218 5 219 52 13 40 | |
9 TTC 251 14 308 87 34 71 | TCC 227 8 241 55 15 49 | TAC 126 7 151 37 18 25 | TGC 150 3 155 45 11 34 | |
10 Leu TTA 131 1 125 33 5 32 | TCA 250 4 275 58 12 47 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 | |
11 TTG 245 6 291 67 18 42 | TCG 104 6 106 19 7 16 | TAG 0 0 0 0 0 0 | Trp TGG 168 9 195 28 18 27 | |
12 -------------------------------------------------------------------------------------------------------------------------------------- | |
13 Leu CTT 171 0 186 54 9 28 | Pro CCT 164 3 170 42 14 40 | His CAT 157 2 143 47 15 41 | Arg CGT 88 5 98 33 10 25 | |
14 CTC 147 9 160 47 20 35 | CCC 81 6 95 16 17 18 | CAC 137 10 158 42 21 32 | CGC 57 16 58 16 29 39 | |
15 CTA 64 0 66 14 5 10 | CCA 232 10 229 63 14 48 | Gln CAA 140 3 126 32 12 28 | CGA 75 18 66 22 19 17 | |
16 CTG 249 18 261 55 25 43 | CCG 65 9 63 6 19 19 | CAG 192 19 213 53 25 51 | CGG 51 4 58 17 12 11 | |
17 -------------------------------------------------------------------------------------------------------------------------------------- | |
18 Ile ATT 173 9 175 60 9 32 | Thr ACT 145 5 140 39 9 40 | Asn AAT 159 5 159 53 12 39 | Ser AGT 146 1 143 44 5 39 | |
19 ATC 218 27 238 54 36 50 | ACC 123 18 154 62 12 36 | AAC 184 17 188 65 26 36 | AGC 160 6 185 36 14 40 | |
20 ATA 186 5 165 68 4 27 | ACA 255 4 262 76 13 40 | Lys AAA 197 11 186 82 22 40 | Arg AGA 165 4 167 59 6 30 | |
21 Met ATG 308 14 341 83 19 67 | ACG 81 6 100 22 8 13 | AAG 224 48 231 53 59 46 | AGG 140 10 150 36 15 23 | |
22 -------------------------------------------------------------------------------------------------------------------------------------- | |
23 Val GTT 176 8 185 40 17 30 | Ala GCT 184 5 184 51 15 40 | Asp GAT 182 5 189 64 15 54 | Gly GGT 160 7 140 40 16 34 | |
24 GTC 200 16 209 42 26 38 | GCC 209 20 224 48 35 49 | GAC 191 16 189 38 30 49 | GGC 164 10 183 21 16 41 | |
25 GTA 166 3 149 50 14 23 | GCA 183 4 176 58 17 34 | Glu GAA 148 6 152 58 16 40 | GGA 163 7 155 35 19 26 | |
26 GTG 224 17 242 40 22 47 | GCG 53 10 53 14 12 17 | GAG 149 20 142 44 36 33 | GGG 80 6 75 8 9 24 | |
27 -------------------------------------------------------------------------------------------------------------------------------------- | |
28 | |
29 Codon position x base (3x4) table for each sequence. | |
30 | |
31 #1: Ac | |
32 position 1: T:0.24656 C:0.20613 A:0.28520 G:0.26210 | |
33 position 2: T:0.31279 C:0.26210 A:0.22744 G:0.19767 | |
34 position 3: T:0.27176 C:0.26140 A:0.23452 G:0.23232 | |
35 Average T:0.27704 C:0.24321 A:0.24905 G:0.23070 | |
36 | |
37 #2: Am | |
38 position 1: T:0.14841 C:0.23322 A:0.33569 G:0.28269 | |
39 position 2: T:0.28269 C:0.21731 A:0.30389 G:0.19611 | |
40 position 3: T:0.14311 C:0.35866 A:0.14134 G:0.35689 | |
41 Average T:0.19140 C:0.26973 A:0.26031 G:0.27856 | |
42 | |
43 #3: Ap | |
44 position 1: T:0.25796 C:0.20504 A:0.28457 G:0.25243 | |
45 position 2: T:0.31986 C:0.26349 A:0.22144 G:0.19521 | |
46 position 3: T:0.26416 C:0.27618 A:0.21924 G:0.24042 | |
47 Average T:0.28066 C:0.24824 A:0.24175 G:0.22935 | |
48 | |
49 #4: Pg | |
50 position 1: T:0.23785 C:0.20268 A:0.32342 G:0.23604 | |
51 position 2: T:0.31255 C:0.25635 A:0.25272 G:0.17839 | |
52 position 3: T:0.28789 C:0.25780 A:0.25671 G:0.19761 | |
53 Average T:0.27943 C:0.23894 A:0.27762 G:0.20401 | |
54 | |
55 #5: Th | |
56 position 1: T:0.17315 C:0.25875 A:0.26167 G:0.30642 | |
57 position 2: T:0.27140 C:0.22082 A:0.30156 G:0.20623 | |
58 position 3: T:0.18093 C:0.35019 A:0.17315 G:0.29572 | |
59 Average T:0.20850 C:0.27659 A:0.24546 G:0.26946 | |
60 | |
61 #6: Ph | |
62 position 1: T:0.23410 C:0.22350 A:0.27558 G:0.26682 | |
63 position 2: T:0.28341 C:0.25991 A:0.24931 G:0.20737 | |
64 position 3: T:0.27972 C:0.29585 A:0.20369 G:0.22074 | |
65 Average T:0.26575 C:0.25975 A:0.24286 G:0.23164 | |
66 | |
67 Sums of codon usage counts | |
68 ------------------------------------------------------------------------------ | |
69 Phe F TTT 622 | Ser S TCT 716 | Tyr Y TAT 255 | Cys C TGT 547 | |
70 TTC 765 | TCC 595 | TAC 364 | TGC 398 | |
71 Leu L TTA 327 | TCA 646 | *** * TAA 0 | *** * TGA 0 | |
72 TTG 669 | TCG 258 | TAG 0 | Trp W TGG 445 | |
73 ------------------------------------------------------------------------------ | |
74 Leu L CTT 448 | Pro P CCT 433 | His H CAT 405 | Arg R CGT 259 | |
75 CTC 418 | CCC 233 | CAC 400 | CGC 215 | |
76 CTA 159 | CCA 596 | Gln Q CAA 341 | CGA 217 | |
77 CTG 651 | CCG 181 | CAG 553 | CGG 153 | |
78 ------------------------------------------------------------------------------ | |
79 Ile I ATT 458 | Thr T ACT 378 | Asn N AAT 427 | Ser S AGT 378 | |
80 ATC 623 | ACC 405 | AAC 516 | AGC 441 | |
81 ATA 455 | ACA 650 | Lys K AAA 538 | Arg R AGA 431 | |
82 Met M ATG 832 | ACG 230 | AAG 661 | AGG 374 | |
83 ------------------------------------------------------------------------------ | |
84 Val V GTT 456 | Ala A GCT 479 | Asp D GAT 509 | Gly G GGT 397 | |
85 GTC 531 | GCC 585 | GAC 513 | GGC 435 | |
86 GTA 405 | GCA 472 | Glu E GAA 420 | GGA 405 | |
87 GTG 592 | GCG 159 | GAG 424 | GGG 202 | |
88 ------------------------------------------------------------------------------ | |
89 | |
90 (Ambiguity data are not used in the counts.) | |
91 | |
92 | |
93 Codon position x base (3x4) table, overall | |
94 | |
95 position 1: T:0.24425 C:0.20932 A:0.28824 G:0.25819 | |
96 position 2: T:0.31094 C:0.25937 A:0.23386 G:0.19582 | |
97 position 3: T:0.26495 C:0.27494 A:0.22410 G:0.23601 | |
98 Average T:0.27338 C:0.24787 A:0.24874 G:0.23001 | |
99 | |
100 | |
101 Nei & Gojobori 1986. dN/dS (dN, dS) | |
102 (Pairwise deletion) | |
103 (Note: This matrix is not used in later ML. analysis. | |
104 Use runmode = -2 for ML pairwise comparison.) | |
105 | |
106 Ac | |
107 Am 0.0436 (0.0628 1.4398) | |
108 Ap 0.4042 (0.0536 0.1327) 0.0340 (0.0422 1.2410) | |
109 Pg 0.2101 (0.1215 0.5783)-1.0000 (0.0396 -1.0000) 0.3864 (0.1403 0.3631) | |
110 Th 0.0067 (0.0137 2.0454)-1.0000 (0.0000 0.0066) 0.0930 (0.0932 1.0019) 0.0156 (0.0625 4.0052) | |
111 Ph 0.1095 (0.0858 0.7837) 0.0387 (0.0613 1.5834) 0.2555 (0.1166 0.4563) 0.6800 (0.1673 0.2459)-1.0000 (-1.0000 -1.0000) | |
112 NOTE: -1 means that NG86 is inapplicable. | |
113 | |
114 | |
115 TREE # 1: (((4, 2), 5), (6, 3), 1); MP score: -1 | |
116 lnL(ntime: 9 np: 11): -71862.094834 +0.000000 | |
117 7..8 8..9 9..4 9..2 8..5 7..10 10..6 10..3 7..1 | |
118 0.246863 0.000004 0.279150 0.179426 0.225632 0.000004 0.478467 0.076909 0.146872 3.015798 0.345817 | |
119 | |
120 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). | |
121 | |
122 tree length = 1.63333 | |
123 | |
124 (((4: 0.279150, 2: 0.179426): 0.000004, 5: 0.225632): 0.246863, (6: 0.478467, 3: 0.076909): 0.000004, 1: 0.146872); | |
125 | |
126 (((Pg: 0.279150, Am: 0.179426): 0.000004, Th: 0.225632): 0.246863, (Ph: 0.478467, Ap: 0.076909): 0.000004, Ac: 0.146872); | |
127 | |
128 Detailed output identifying parameters | |
129 | |
130 kappa (ts/tv) = 3.01580 | |
131 | |
132 omega (dN/dS) = 0.34582 | |
133 | |
134 dN & dS for each branch | |
135 | |
136 branch t N S dN/dS dN dS N*dN S*dS | |
137 | |
138 7..8 0.247 29225.7 12036.3 0.3458 0.0530 0.1533 1549.7 1845.6 | |
139 8..9 0.000 29225.7 12036.3 0.3458 0.0000 0.0000 0.0 0.0 | |
140 9..4 0.279 29225.7 12036.3 0.3458 0.0600 0.1734 1752.4 2087.0 | |
141 9..2 0.179 29225.7 12036.3 0.3458 0.0385 0.1114 1126.4 1341.4 | |
142 8..5 0.226 29225.7 12036.3 0.3458 0.0485 0.1401 1416.5 1686.9 | |
143 7..10 0.000 29225.7 12036.3 0.3458 0.0000 0.0000 0.0 0.0 | |
144 10..6 0.478 29225.7 12036.3 0.3458 0.1028 0.2972 3003.7 3577.1 | |
145 10..3 0.077 29225.7 12036.3 0.3458 0.0165 0.0478 482.8 575.0 | |
146 7..1 0.147 29225.7 12036.3 0.3458 0.0315 0.0912 922.0 1098.1 | |
147 | |
148 tree length for dN: 0.3508 | |
149 tree length for dS: 1.0145 | |
150 | |
151 | |
152 Time used: 1:09 |