Mercurial > repos > iuc > codeml

annotate 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
parents
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0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
1 CODONML (in paml version 4.9, March 2015) /tmp/tmpMdbfK7/files/000/dataset_12.dat
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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2 Model: several dN/dS ratios for branches for branches,
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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3 Codon frequency model: F1x4
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
4 ns = 6 ls = 13754
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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5
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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6 Codon usage in sequences
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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7 --------------------------------------------------------------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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12 --------------------------------------------------------------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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17 --------------------------------------------------------------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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22 --------------------------------------------------------------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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27 --------------------------------------------------------------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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28
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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29 Codon position x base (3x4) table for each sequence.
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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30
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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31 #1: Ac
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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32 position 1: T:0.24656 C:0.20613 A:0.28520 G:0.26210
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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33 position 2: T:0.31279 C:0.26210 A:0.22744 G:0.19767
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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34 position 3: T:0.27176 C:0.26140 A:0.23452 G:0.23232
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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35 Average T:0.27704 C:0.24321 A:0.24905 G:0.23070
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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36
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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37 #2: Am
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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38 position 1: T:0.14841 C:0.23322 A:0.33569 G:0.28269
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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39 position 2: T:0.28269 C:0.21731 A:0.30389 G:0.19611
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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40 position 3: T:0.14311 C:0.35866 A:0.14134 G:0.35689
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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41 Average T:0.19140 C:0.26973 A:0.26031 G:0.27856
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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42
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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43 #3: Ap
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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44 position 1: T:0.25796 C:0.20504 A:0.28457 G:0.25243
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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45 position 2: T:0.31986 C:0.26349 A:0.22144 G:0.19521
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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46 position 3: T:0.26416 C:0.27618 A:0.21924 G:0.24042
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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47 Average T:0.28066 C:0.24824 A:0.24175 G:0.22935
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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48
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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49 #4: Pg
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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50 position 1: T:0.23785 C:0.20268 A:0.32342 G:0.23604
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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51 position 2: T:0.31255 C:0.25635 A:0.25272 G:0.17839
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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52 position 3: T:0.28789 C:0.25780 A:0.25671 G:0.19761
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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53 Average T:0.27943 C:0.23894 A:0.27762 G:0.20401
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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54
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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55 #5: Th
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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56 position 1: T:0.17315 C:0.25875 A:0.26167 G:0.30642
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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57 position 2: T:0.27140 C:0.22082 A:0.30156 G:0.20623
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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58 position 3: T:0.18093 C:0.35019 A:0.17315 G:0.29572
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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59 Average T:0.20850 C:0.27659 A:0.24546 G:0.26946
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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60
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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61 #6: Ph
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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62 position 1: T:0.23410 C:0.22350 A:0.27558 G:0.26682
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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63 position 2: T:0.28341 C:0.25991 A:0.24931 G:0.20737
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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64 position 3: T:0.27972 C:0.29585 A:0.20369 G:0.22074
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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65 Average T:0.26575 C:0.25975 A:0.24286 G:0.23164
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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66
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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67 Sums of codon usage counts
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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68 ------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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69 Phe F TTT 622 | Ser S TCT 716 | Tyr Y TAT 255 | Cys C TGT 547
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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70 TTC 765 | TCC 595 | TAC 364 | TGC 398
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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71 Leu L TTA 327 | TCA 646 | *** * TAA 0 | *** * TGA 0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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72 TTG 669 | TCG 258 | TAG 0 | Trp W TGG 445
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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73 ------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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74 Leu L CTT 448 | Pro P CCT 433 | His H CAT 405 | Arg R CGT 259
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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75 CTC 418 | CCC 233 | CAC 400 | CGC 215
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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76 CTA 159 | CCA 596 | Gln Q CAA 341 | CGA 217
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
77 CTG 651 | CCG 181 | CAG 553 | CGG 153
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
78 ------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
79 Ile I ATT 458 | Thr T ACT 378 | Asn N AAT 427 | Ser S AGT 378
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
80 ATC 623 | ACC 405 | AAC 516 | AGC 441
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
81 ATA 455 | ACA 650 | Lys K AAA 538 | Arg R AGA 431
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
82 Met M ATG 832 | ACG 230 | AAG 661 | AGG 374
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
83 ------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
84 Val V GTT 456 | Ala A GCT 479 | Asp D GAT 509 | Gly G GGT 397
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
85 GTC 531 | GCC 585 | GAC 513 | GGC 435
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
86 GTA 405 | GCA 472 | Glu E GAA 420 | GGA 405
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
87 GTG 592 | GCG 159 | GAG 424 | GGG 202
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
88 ------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
89
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
90 (Ambiguity data are not used in the counts.)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
91
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
92
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
93 Codon position x base (3x4) table, overall
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
94
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
95 position 1: T:0.24425 C:0.20932 A:0.28824 G:0.25819
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
96 position 2: T:0.31094 C:0.25937 A:0.23386 G:0.19582
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
97 position 3: T:0.26495 C:0.27494 A:0.22410 G:0.23601
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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98 Average T:0.27338 C:0.24787 A:0.24874 G:0.23001
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
99
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
100
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
101 Nei & Gojobori 1986. dN/dS (dN, dS)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
102 (Pairwise deletion)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
103 (Note: This matrix is not used in later ML. analysis.
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
104 Use runmode = -2 for ML pairwise comparison.)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
105
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
106 Ac
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
107 Am 0.0436 (0.0628 1.4398)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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108 Ap 0.4042 (0.0536 0.1327) 0.0340 (0.0422 1.2410)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
109 Pg 0.2101 (0.1215 0.5783)-1.0000 (0.0396 -1.0000) 0.3864 (0.1403 0.3631)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
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)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
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)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
112 NOTE: -1 means that NG86 is inapplicable.
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
113
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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114
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
115 TREE # 1: (((4, 2), 5), (6, 3), 1); MP score: -1
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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116 lnL(ntime: 9 np: 14): -71787.227810 +0.000000
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
117 7..8 8..9 9..4 9..2 8..5 7..10 10..6 10..3 7..1
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
119
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
120 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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121
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
122 tree length = 1.83334
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
123
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
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);
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
125
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
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);
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
127
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
128 Detailed output identifying parameters
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
129
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
130 kappa (ts/tv) = 3.03432
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
131
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
132 w (dN/dS) for branches: 0.53952 0.33269 0.08710 0.03412
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
133
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
134 dN & dS for each branch
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
135
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
136 branch t N S dN/dS dN dS N*dN S*dS
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
137
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
138 7..8 0.289 29216.6 12045.4 0.5395 0.0772 0.1431 2255.0 1723.2
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
139 8..9 0.000 29216.6 12045.4 0.0871 0.0000 0.0000 0.0 0.0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
140 9..4 0.220 29216.6 12045.4 0.0871 0.0180 0.2071 527.0 2494.5
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
141 9..2 0.262 29216.6 12045.4 0.0871 0.0215 0.2470 628.6 2975.4
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
142 8..5 0.351 29216.6 12045.4 0.0341 0.0126 0.3700 368.8 4456.6
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
143 7..10 0.000 29216.6 12045.4 0.3327 0.0000 0.0000 0.0 0.0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
144 10..6 0.491 29216.6 12045.4 0.3327 0.1032 0.3103 3016.4 3738.0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
145 10..3 0.068 29216.6 12045.4 0.3327 0.0143 0.0430 417.7 517.7
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
146 7..1 0.152 29216.6 12045.4 0.5395 0.0407 0.0754 1188.4 908.1
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
147
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
148 tree length for dN: 0.2876
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
149 tree length for dS: 1.3959
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
150
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
151 dS tree:
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
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);
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
153 dN tree:
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
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);
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
155
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
156 w ratios as labels for TreeView:
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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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 );
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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