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comparison test-data/3_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_23.dat
2 Model: NSbranch3 for branches,
3 Codon frequency model: F1x4
4 Site-class models: PositiveSelection
5 ns = 6 ls = 13754
6
7 Codon usage in sequences
8 --------------------------------------------------------------------------------------------------------------------------------------
9 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
10 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
11 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
12 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
13 --------------------------------------------------------------------------------------------------------------------------------------
14 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
15 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
16 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
17 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
18 --------------------------------------------------------------------------------------------------------------------------------------
19 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
20 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
21 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
22 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
23 --------------------------------------------------------------------------------------------------------------------------------------
24 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
25 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
26 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
27 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
28 --------------------------------------------------------------------------------------------------------------------------------------
29
30 Codon position x base (3x4) table for each sequence.
31
32 #1: Ac
33 position 1: T:0.24656 C:0.20613 A:0.28520 G:0.26210
34 position 2: T:0.31279 C:0.26210 A:0.22744 G:0.19767
35 position 3: T:0.27176 C:0.26140 A:0.23452 G:0.23232
36 Average T:0.27704 C:0.24321 A:0.24905 G:0.23070
37
38 #2: Am
39 position 1: T:0.14841 C:0.23322 A:0.33569 G:0.28269
40 position 2: T:0.28269 C:0.21731 A:0.30389 G:0.19611
41 position 3: T:0.14311 C:0.35866 A:0.14134 G:0.35689
42 Average T:0.19140 C:0.26973 A:0.26031 G:0.27856
43
44 #3: Ap
45 position 1: T:0.25796 C:0.20504 A:0.28457 G:0.25243
46 position 2: T:0.31986 C:0.26349 A:0.22144 G:0.19521
47 position 3: T:0.26416 C:0.27618 A:0.21924 G:0.24042
48 Average T:0.28066 C:0.24824 A:0.24175 G:0.22935
49
50 #4: Pg
51 position 1: T:0.23785 C:0.20268 A:0.32342 G:0.23604
52 position 2: T:0.31255 C:0.25635 A:0.25272 G:0.17839
53 position 3: T:0.28789 C:0.25780 A:0.25671 G:0.19761
54 Average T:0.27943 C:0.23894 A:0.27762 G:0.20401
55
56 #5: Th
57 position 1: T:0.17315 C:0.25875 A:0.26167 G:0.30642
58 position 2: T:0.27140 C:0.22082 A:0.30156 G:0.20623
59 position 3: T:0.18093 C:0.35019 A:0.17315 G:0.29572
60 Average T:0.20850 C:0.27659 A:0.24546 G:0.26946
61
62 #6: Ph
63 position 1: T:0.23410 C:0.22350 A:0.27558 G:0.26682
64 position 2: T:0.28341 C:0.25991 A:0.24931 G:0.20737
65 position 3: T:0.27972 C:0.29585 A:0.20369 G:0.22074
66 Average T:0.26575 C:0.25975 A:0.24286 G:0.23164
67
68 Sums of codon usage counts
69 ------------------------------------------------------------------------------
70 Phe F TTT 622 | Ser S TCT 716 | Tyr Y TAT 255 | Cys C TGT 547
71 TTC 765 | TCC 595 | TAC 364 | TGC 398
72 Leu L TTA 327 | TCA 646 | *** * TAA 0 | *** * TGA 0
73 TTG 669 | TCG 258 | TAG 0 | Trp W TGG 445
74 ------------------------------------------------------------------------------
75 Leu L CTT 448 | Pro P CCT 433 | His H CAT 405 | Arg R CGT 259
76 CTC 418 | CCC 233 | CAC 400 | CGC 215
77 CTA 159 | CCA 596 | Gln Q CAA 341 | CGA 217
78 CTG 651 | CCG 181 | CAG 553 | CGG 153
79 ------------------------------------------------------------------------------
80 Ile I ATT 458 | Thr T ACT 378 | Asn N AAT 427 | Ser S AGT 378
81 ATC 623 | ACC 405 | AAC 516 | AGC 441
82 ATA 455 | ACA 650 | Lys K AAA 538 | Arg R AGA 431
83 Met M ATG 832 | ACG 230 | AAG 661 | AGG 374
84 ------------------------------------------------------------------------------
85 Val V GTT 456 | Ala A GCT 479 | Asp D GAT 509 | Gly G GGT 397
86 GTC 531 | GCC 585 | GAC 513 | GGC 435
87 GTA 405 | GCA 472 | Glu E GAA 420 | GGA 405
88 GTG 592 | GCG 159 | GAG 424 | GGG 202
89 ------------------------------------------------------------------------------
90
91 (Ambiguity data are not used in the counts.)
92
93
94 Codon position x base (3x4) table, overall
95
96 position 1: T:0.24425 C:0.20932 A:0.28824 G:0.25819
97 position 2: T:0.31094 C:0.25937 A:0.23386 G:0.19582
98 position 3: T:0.26495 C:0.27494 A:0.22410 G:0.23601
99 Average T:0.27338 C:0.24787 A:0.24874 G:0.23001
100
101
102 Nei & Gojobori 1986. dN/dS (dN, dS)
103 (Pairwise deletion)
104 (Note: This matrix is not used in later ML. analysis.
105 Use runmode = -2 for ML pairwise comparison.)
106
107 Ac
108 Am 0.0436 (0.0628 1.4398)
109 Ap 0.4042 (0.0536 0.1327) 0.0340 (0.0422 1.2410)
110 Pg 0.2101 (0.1215 0.5783)-1.0000 (0.0396 -1.0000) 0.3864 (0.1403 0.3631)
111 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)
112 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)
113 NOTE: -1 means that NG86 is inapplicable.
114
115
116 TREE # 1: (((4, 2), 5), (6, 3), 1); MP score: -1
117 lnL(ntime: 9 np: 15): -71845.285288 +0.000000
118 7..8 8..9 9..4 9..2 8..5 7..10 10..6 10..3 7..1
119 0.253789 0.000004 0.294642 0.199868 0.242499 0.000004 0.471201 0.102634 0.122472 3.060446 0.693669 0.106076 0.279090 0.015724 0.820701
120
121 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
122
123 tree length = 1.68711
124
125 (((4: 0.294642, 2: 0.199868): 0.000004, 5: 0.242499): 0.253789, (6: 0.471201, 3: 0.102634): 0.000004, 1: 0.122472);
126
127 (((Pg: 0.294642, Am: 0.199868): 0.000004, Th: 0.242499): 0.253789, (Ph: 0.471201, Ap: 0.102634): 0.000004, Ac: 0.122472);
128
129 Detailed output identifying parameters
130
131 kappa (ts/tv) = 3.06045
132
133
134 MLEs of dN/dS (w) for site classes (K=3)
135
136 site class 0 1 2
137 proportion 0.69367 0.10608 0.20025
138 branch type 0: 0.27909 1.00000 0.01572
139 branch type 1: 0.27909 1.00000 0.82070
140
141
142 Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
143
144 The grid (see ternary graph for p0-p1)
145
146 w0: 0.050 0.150 0.250 0.350 0.450 0.550 0.650 0.750 0.850 0.950
147 w2: 0.150 0.450 0.750 1.050 1.350 1.650 1.950 2.250 2.550 2.850
148 w3: 0.150 0.450 0.750 1.050 1.350 1.650 1.950 2.250 2.550 2.850
149
150
151 Posterior on the grid
152
153 w0: 0.000 0.016 0.738 0.171 0.066 0.006 0.002 0.000 0.000 0.000
154 w2: 0.988 0.012 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
155 w3: 0.000 0.828 0.064 0.033 0.057 0.014 0.001 0.001 0.000 0.001
156
157 Posterior for p0-p1 (see the ternary graph) (YWN2015, fig. 1)
158
159 0.000
160 0.000 0.000 0.000
161 0.000 0.000 0.000 0.000 0.000
162 0.000 0.000 0.000 0.000 0.000 0.000 0.000
163 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
164 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
165 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
166 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
167 0.001 0.001 0.010 0.010 0.072 0.038 0.202 0.053 0.170 0.020 0.034 0.002 0.046 0.000 0.006 0.000 0.000
168 0.000 0.000 0.000 0.003 0.004 0.039 0.014 0.031 0.010 0.101 0.007 0.020 0.001 0.026 0.001 0.072 0.003 0.001 0.000
169
170 sum of density on p0-p1 = 1.000000
171
172 Time used: 4:22