Mercurial > repos > iuc > codeml

annotate 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
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_23.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: NSbranch3 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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4 Site-class models: PositiveSelection
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
5 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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6
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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7 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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8 --------------------------------------------------------------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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13 --------------------------------------------------------------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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18 --------------------------------------------------------------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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23 --------------------------------------------------------------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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28 --------------------------------------------------------------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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29
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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30 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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31
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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32 #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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33 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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34 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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35 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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36 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
iuc
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37
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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38 #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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39 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
parents:
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40 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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41 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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42 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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43
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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44 #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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45 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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46 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
parents:
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47 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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48 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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49
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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50 #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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51 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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52 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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53 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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54 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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55
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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56 #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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57 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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58 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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59 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
parents:
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60 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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61
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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62 #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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63 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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64 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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65 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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66 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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67
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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68 Sums of codon usage counts
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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69 ------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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70 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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71 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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72 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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73 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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74 ------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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75 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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76 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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77 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
parents:
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78 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
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79 ------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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80 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:
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81 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:
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82 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:
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83 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
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84 ------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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85 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:
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86 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
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87 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
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88 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
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89 ------------------------------------------------------------------------------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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90
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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91 (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
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92
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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93
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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94 Codon position x base (3x4) table, overall
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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95
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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96 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
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97 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
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98 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
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99 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
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100
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101
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102 Nei & Gojobori 1986. dN/dS (dN, dS)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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103 (Pairwise deletion)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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104 (Note: This matrix is not used in later ML. analysis.
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105 Use runmode = -2 for ML pairwise comparison.)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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106
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107 Ac
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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108 Am 0.0436 (0.0628 1.4398)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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109 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
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110 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
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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)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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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)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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113 NOTE: -1 means that NG86 is inapplicable.
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114
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115
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116 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
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117 lnL(ntime: 9 np: 15): -71845.285288 +0.000000
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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118 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
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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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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120
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121 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
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122
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iuc
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123 tree length = 1.68711
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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124
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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);
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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126
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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);
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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128
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129 Detailed output identifying parameters
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130
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131 kappa (ts/tv) = 3.06045
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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132
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133
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134 MLEs of dN/dS (w) for site classes (K=3)
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135
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136 site class 0 1 2
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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137 proportion 0.69367 0.10608 0.20025
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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138 branch type 0: 0.27909 1.00000 0.01572
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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139 branch type 1: 0.27909 1.00000 0.82070
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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140
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141
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142 Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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143
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144 The grid (see ternary graph for p0-p1)
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145
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146 w0: 0.050 0.150 0.250 0.350 0.450 0.550 0.650 0.750 0.850 0.950
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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147 w2: 0.150 0.450 0.750 1.050 1.350 1.650 1.950 2.250 2.550 2.850
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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148 w3: 0.150 0.450 0.750 1.050 1.350 1.650 1.950 2.250 2.550 2.850
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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149
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150
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151 Posterior on the grid
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152
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153 w0: 0.000 0.016 0.738 0.171 0.066 0.006 0.002 0.000 0.000 0.000
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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154 w2: 0.988 0.012 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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155 w3: 0.000 0.828 0.064 0.033 0.057 0.014 0.001 0.001 0.000 0.001
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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156
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157 Posterior for p0-p1 (see the ternary graph) (YWN2015, fig. 1)
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158
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diff changeset
159 0.000
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
160 0.000 0.000 0.000
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
161 0.000 0.000 0.000 0.000 0.000
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
162 0.000 0.000 0.000 0.000 0.000 0.000 0.000
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
163 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
164 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
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
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
169
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
170 sum of density on p0-p1 = 1.000000
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
171
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
172 Time used: 4:22