Mercurial > repos > iuc > codeml
changeset 3:b2b8e75a962d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b"
| author | iuc |
|---|---|
| date | Wed, 16 Sep 2020 16:46:06 +0000 |
| parents | 66228e9c29d9 |
| children | f9cb3a4339c2 |
| files | codeml.xml test-data/1_run_codeml test-data/2_run_codeml test-data/3_run_codeml test-data/empty |
| diffstat | 4 files changed, 18 insertions(+), 487 deletions(-) [+] |
line wrap: on
line diff
--- a/codeml.xml Thu Dec 26 05:34:15 2019 -0500 +++ b/codeml.xml Wed Sep 16 16:46:06 2020 +0000 @@ -271,7 +271,12 @@ <output name="2ngdn" value="1_2ngdn" /> <output name="2ngds" value="1_2ngds" /> <output name="2ngt" value="1_2ngt" /> - <output name="run" value="1_run_codeml" lines_diff="20"/> + <output name="run"> + <assert_contents> + <has_text text="CODONML (in paml version 4.9, March 2015)"/> + <has_text text="Time used:" /> + </assert_contents> + </output> <output name="ctl" value="1_codeml.ctl" lines_diff="4" /> </test> <test> @@ -287,7 +292,12 @@ <output name="2ngdn" value="2_2ngdn" /> <output name="2ngds" value="2_2ngds" /> <output name="2ngt" value="2_2ngt" /> - <output name="run" value="2_run_codeml" lines_diff="20" /> + <output name="run"> + <assert_contents> + <has_text text="CODONML (in paml version 4.9, March 2015)"/> + <has_text text="Time used:" /> + </assert_contents> + </output> <output name="ctl" value="2_codeml.ctl" lines_diff="4" /> </test> <test> @@ -303,7 +313,12 @@ <output name="2ngdn" value="3_2ngdn" /> <output name="2ngds" value="3_2ngds" /> <output name="2ngt" value="3_2ngt" /> - <output name="run" value="3_run_codeml" lines_diff="20"/> + <output name="run"> + <assert_contents> + <has_text text="CODONML (in paml version 4.9, March 2015)"/> + <has_text text="Time used:" /> + </assert_contents> + </output> <output name="ctl" value="3_codeml.ctl" lines_diff="4" /> </test> </tests>
--- a/test-data/1_run_codeml Thu Dec 26 05:34:15 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,152 +0,0 @@ -CODONML (in paml version 4.9, March 2015) /tmp/tmpMdbfK7/files/000/dataset_1.dat -Model: One dN/dS ratio for branches, -Codon frequency model: F1x4 -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: 11): -71862.094834 +0.000000 - 7..8 8..9 9..4 9..2 8..5 7..10 10..6 10..3 7..1 - 0.246863 0.000004 0.279150 0.179426 0.225632 0.000004 0.478467 0.076909 0.146872 3.015798 0.345817 - -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 1.63333 - -(((4: 0.279150, 2: 0.179426): 0.000004, 5: 0.225632): 0.246863, (6: 0.478467, 3: 0.076909): 0.000004, 1: 0.146872); - -(((Pg: 0.279150, Am: 0.179426): 0.000004, Th: 0.225632): 0.246863, (Ph: 0.478467, Ap: 0.076909): 0.000004, Ac: 0.146872); - -Detailed output identifying parameters - -kappa (ts/tv) = 3.01580 - -omega (dN/dS) = 0.34582 - -dN & dS for each branch - - branch t N S dN/dS dN dS N*dN S*dS - - 7..8 0.247 29225.7 12036.3 0.3458 0.0530 0.1533 1549.7 1845.6 - 8..9 0.000 29225.7 12036.3 0.3458 0.0000 0.0000 0.0 0.0 - 9..4 0.279 29225.7 12036.3 0.3458 0.0600 0.1734 1752.4 2087.0 - 9..2 0.179 29225.7 12036.3 0.3458 0.0385 0.1114 1126.4 1341.4 - 8..5 0.226 29225.7 12036.3 0.3458 0.0485 0.1401 1416.5 1686.9 - 7..10 0.000 29225.7 12036.3 0.3458 0.0000 0.0000 0.0 0.0 - 10..6 0.478 29225.7 12036.3 0.3458 0.1028 0.2972 3003.7 3577.1 - 10..3 0.077 29225.7 12036.3 0.3458 0.0165 0.0478 482.8 575.0 - 7..1 0.147 29225.7 12036.3 0.3458 0.0315 0.0912 922.0 1098.1 - -tree length for dN: 0.3508 -tree length for dS: 1.0145 - - -Time used: 1:09
--- a/test-data/2_run_codeml Thu Dec 26 05:34:15 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,160 +0,0 @@ -CODONML (in paml version 4.9, March 2015) /tmp/tmpMdbfK7/files/000/dataset_12.dat -Model: several dN/dS ratios for branches for branches, -Codon frequency model: F1x4 -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: 14): -71787.227810 +0.000000 - 7..8 8..9 9..4 9..2 8..5 7..10 10..6 10..3 7..1 - 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 - -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 1.83334 - -(((4: 0.219684, 2: 0.262034): 0.000004, 5: 0.350843): 0.289241, (6: 0.491088, 3: 0.068009): 0.000004, 1: 0.152428); - -(((Pg: 0.219684, Am: 0.262034): 0.000004, Th: 0.350843): 0.289241, (Ph: 0.491088, Ap: 0.068009): 0.000004, Ac: 0.152428); - -Detailed output identifying parameters - -kappa (ts/tv) = 3.03432 - -w (dN/dS) for branches: 0.53952 0.33269 0.08710 0.03412 - -dN & dS for each branch - - branch t N S dN/dS dN dS N*dN S*dS - - 7..8 0.289 29216.6 12045.4 0.5395 0.0772 0.1431 2255.0 1723.2 - 8..9 0.000 29216.6 12045.4 0.0871 0.0000 0.0000 0.0 0.0 - 9..4 0.220 29216.6 12045.4 0.0871 0.0180 0.2071 527.0 2494.5 - 9..2 0.262 29216.6 12045.4 0.0871 0.0215 0.2470 628.6 2975.4 - 8..5 0.351 29216.6 12045.4 0.0341 0.0126 0.3700 368.8 4456.6 - 7..10 0.000 29216.6 12045.4 0.3327 0.0000 0.0000 0.0 0.0 - 10..6 0.491 29216.6 12045.4 0.3327 0.1032 0.3103 3016.4 3738.0 - 10..3 0.068 29216.6 12045.4 0.3327 0.0143 0.0430 417.7 517.7 - 7..1 0.152 29216.6 12045.4 0.5395 0.0407 0.0754 1188.4 908.1 - -tree length for dN: 0.2876 -tree length for dS: 1.3959 - -dS tree: -(((Pg: 0.207095, Am: 0.247017): 0.000004, Th: 0.369987): 0.143059, (Ph: 0.310329, Ap: 0.042976): 0.000003, Ac: 0.075391); -dN tree: -(((Pg: 0.018038, Am: 0.021515): 0.000000, Th: 0.012624): 0.077183, (Ph: 0.103242, Ap: 0.014298): 0.000001, Ac: 0.040675); - -w ratios as labels for TreeView: -(((Pg #0.0870978 , Am #0.0870978 ) #0.0870978 , Th #0.0341211 ) #0.53952 , (Ph #0.332686 , Ap #0.332686 ) #0.332686 , Ac #0.53952 ); - - -Time used: 2:11
--- a/test-data/3_run_codeml Thu Dec 26 05:34:15 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,172 +0,0 @@ -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