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comparison test-data/2_run_codeml @ 0:961a712f9743 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
author iuc
date Tue, 29 Aug 2017 19:12:01 -0400
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-1:000000000000 0:961a712f9743
1 CODONML (in paml version 4.9, March 2015) /tmp/tmpMdbfK7/files/000/dataset_12.dat
2 Model: several dN/dS ratios for branches 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: 14): -71787.227810 +0.000000
117 7..8 8..9 9..4 9..2 8..5 7..10 10..6 10..3 7..1
118 0.289241 0.000004 0.219684 0.262034 0.350843 0.000004 0.491088 0.068009 0.152428 3.034323 0.539520 0.332686 0.087098 0.034121
119
120 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
121
122 tree length = 1.83334
123
124 (((4: 0.219684, 2: 0.262034): 0.000004, 5: 0.350843): 0.289241, (6: 0.491088, 3: 0.068009): 0.000004, 1: 0.152428);
125
126 (((Pg: 0.219684, Am: 0.262034): 0.000004, Th: 0.350843): 0.289241, (Ph: 0.491088, Ap: 0.068009): 0.000004, Ac: 0.152428);
127
128 Detailed output identifying parameters
129
130 kappa (ts/tv) = 3.03432
131
132 w (dN/dS) for branches: 0.53952 0.33269 0.08710 0.03412
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 0.289 29216.6 12045.4 0.5395 0.0772 0.1431 2255.0 1723.2
139 8..9 0.000 29216.6 12045.4 0.0871 0.0000 0.0000 0.0 0.0
140 9..4 0.220 29216.6 12045.4 0.0871 0.0180 0.2071 527.0 2494.5
141 9..2 0.262 29216.6 12045.4 0.0871 0.0215 0.2470 628.6 2975.4
142 8..5 0.351 29216.6 12045.4 0.0341 0.0126 0.3700 368.8 4456.6
143 7..10 0.000 29216.6 12045.4 0.3327 0.0000 0.0000 0.0 0.0
144 10..6 0.491 29216.6 12045.4 0.3327 0.1032 0.3103 3016.4 3738.0
145 10..3 0.068 29216.6 12045.4 0.3327 0.0143 0.0430 417.7 517.7
146 7..1 0.152 29216.6 12045.4 0.5395 0.0407 0.0754 1188.4 908.1
147
148 tree length for dN: 0.2876
149 tree length for dS: 1.3959
150
151 dS tree:
152 (((Pg: 0.207095, Am: 0.247017): 0.000004, Th: 0.369987): 0.143059, (Ph: 0.310329, Ap: 0.042976): 0.000003, Ac: 0.075391);
153 dN tree:
154 (((Pg: 0.018038, Am: 0.021515): 0.000000, Th: 0.012624): 0.077183, (Ph: 0.103242, Ap: 0.014298): 0.000001, Ac: 0.040675);
155
156 w ratios as labels for TreeView:
157 (((Pg #0.0870978 , Am #0.0870978 ) #0.0870978 , Th #0.0341211 ) #0.53952 , (Ph #0.332686 , Ap #0.332686 ) #0.332686 , Ac #0.53952 );
158
159
160 Time used: 2:11