Mercurial > repos > iuc > codeml
diff test-data/3_run_codeml @ 0:961a712f9743 draft
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 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3_run_codeml Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,172 @@ +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