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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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CODONML (in paml version 4.9, March 2015) /tmp/tmpMdbfK7/files/000/dataset_23.dat Model: NSbranch3 for branches, Codon frequency model: F1x4 Site-class models: PositiveSelection ns = 6 ls = 13754 Codon usage in sequences -------------------------------------------------------------------------------------------------------------------------------------- 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 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 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 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 -------------------------------------------------------------------------------------------------------------------------------------- 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 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 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 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 -------------------------------------------------------------------------------------------------------------------------------------- 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 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 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 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 -------------------------------------------------------------------------------------------------------------------------------------- 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 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 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 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 -------------------------------------------------------------------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: Ac position 1: T:0.24656 C:0.20613 A:0.28520 G:0.26210 position 2: T:0.31279 C:0.26210 A:0.22744 G:0.19767 position 3: T:0.27176 C:0.26140 A:0.23452 G:0.23232 Average T:0.27704 C:0.24321 A:0.24905 G:0.23070 #2: Am position 1: T:0.14841 C:0.23322 A:0.33569 G:0.28269 position 2: T:0.28269 C:0.21731 A:0.30389 G:0.19611 position 3: T:0.14311 C:0.35866 A:0.14134 G:0.35689 Average T:0.19140 C:0.26973 A:0.26031 G:0.27856 #3: Ap position 1: T:0.25796 C:0.20504 A:0.28457 G:0.25243 position 2: T:0.31986 C:0.26349 A:0.22144 G:0.19521 position 3: T:0.26416 C:0.27618 A:0.21924 G:0.24042 Average T:0.28066 C:0.24824 A:0.24175 G:0.22935 #4: Pg position 1: T:0.23785 C:0.20268 A:0.32342 G:0.23604 position 2: T:0.31255 C:0.25635 A:0.25272 G:0.17839 position 3: T:0.28789 C:0.25780 A:0.25671 G:0.19761 Average T:0.27943 C:0.23894 A:0.27762 G:0.20401 #5: Th position 1: T:0.17315 C:0.25875 A:0.26167 G:0.30642 position 2: T:0.27140 C:0.22082 A:0.30156 G:0.20623 position 3: T:0.18093 C:0.35019 A:0.17315 G:0.29572 Average T:0.20850 C:0.27659 A:0.24546 G:0.26946 #6: Ph position 1: T:0.23410 C:0.22350 A:0.27558 G:0.26682 position 2: T:0.28341 C:0.25991 A:0.24931 G:0.20737 position 3: T:0.27972 C:0.29585 A:0.20369 G:0.22074 Average T:0.26575 C:0.25975 A:0.24286 G:0.23164 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 622 | Ser S TCT 716 | Tyr Y TAT 255 | Cys C TGT 547 TTC 765 | TCC 595 | TAC 364 | TGC 398 Leu L TTA 327 | TCA 646 | *** * TAA 0 | *** * TGA 0 TTG 669 | TCG 258 | TAG 0 | Trp W TGG 445 ------------------------------------------------------------------------------ Leu L CTT 448 | Pro P CCT 433 | His H CAT 405 | Arg R CGT 259 CTC 418 | CCC 233 | CAC 400 | CGC 215 CTA 159 | CCA 596 | Gln Q CAA 341 | CGA 217 CTG 651 | CCG 181 | CAG 553 | CGG 153 ------------------------------------------------------------------------------ Ile I ATT 458 | Thr T ACT 378 | Asn N AAT 427 | Ser S AGT 378 ATC 623 | ACC 405 | AAC 516 | AGC 441 ATA 455 | ACA 650 | Lys K AAA 538 | Arg R AGA 431 Met M ATG 832 | ACG 230 | AAG 661 | AGG 374 ------------------------------------------------------------------------------ Val V GTT 456 | Ala A GCT 479 | Asp D GAT 509 | Gly G GGT 397 GTC 531 | GCC 585 | GAC 513 | GGC 435 GTA 405 | GCA 472 | Glu E GAA 420 | GGA 405 GTG 592 | GCG 159 | GAG 424 | GGG 202 ------------------------------------------------------------------------------ (Ambiguity data are not used in the counts.) Codon position x base (3x4) table, overall position 1: T:0.24425 C:0.20932 A:0.28824 G:0.25819 position 2: T:0.31094 C:0.25937 A:0.23386 G:0.19582 position 3: T:0.26495 C:0.27494 A:0.22410 G:0.23601 Average T:0.27338 C:0.24787 A:0.24874 G:0.23001 Nei & Gojobori 1986. dN/dS (dN, dS) (Pairwise deletion) (Note: This matrix is not used in later ML. analysis. Use runmode = -2 for ML pairwise comparison.) Ac Am 0.0436 (0.0628 1.4398) Ap 0.4042 (0.0536 0.1327) 0.0340 (0.0422 1.2410) Pg 0.2101 (0.1215 0.5783)-1.0000 (0.0396 -1.0000) 0.3864 (0.1403 0.3631) 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) 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) NOTE: -1 means that NG86 is inapplicable. TREE # 1: (((4, 2), 5), (6, 3), 1); MP score: -1 lnL(ntime: 9 np: 15): -71845.285288 +0.000000 7..8 8..9 9..4 9..2 8..5 7..10 10..6 10..3 7..1 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 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 1.68711 (((4: 0.294642, 2: 0.199868): 0.000004, 5: 0.242499): 0.253789, (6: 0.471201, 3: 0.102634): 0.000004, 1: 0.122472); (((Pg: 0.294642, Am: 0.199868): 0.000004, Th: 0.242499): 0.253789, (Ph: 0.471201, Ap: 0.102634): 0.000004, Ac: 0.122472); Detailed output identifying parameters kappa (ts/tv) = 3.06045 MLEs of dN/dS (w) for site classes (K=3) site class 0 1 2 proportion 0.69367 0.10608 0.20025 branch type 0: 0.27909 1.00000 0.01572 branch type 1: 0.27909 1.00000 0.82070 Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) The grid (see ternary graph for p0-p1) w0: 0.050 0.150 0.250 0.350 0.450 0.550 0.650 0.750 0.850 0.950 w2: 0.150 0.450 0.750 1.050 1.350 1.650 1.950 2.250 2.550 2.850 w3: 0.150 0.450 0.750 1.050 1.350 1.650 1.950 2.250 2.550 2.850 Posterior on the grid w0: 0.000 0.016 0.738 0.171 0.066 0.006 0.002 0.000 0.000 0.000 w2: 0.988 0.012 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 w3: 0.000 0.828 0.064 0.033 0.057 0.014 0.001 0.001 0.000 0.001 Posterior for p0-p1 (see the ternary graph) (YWN2015, fig. 1) 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 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 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 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 0.000 0.000 0.000 0.000 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 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 sum of density on p0-p1 = 1.000000 Time used: 4:22