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annotate snpEff/snpEff.config @ 1:2cf01e805427

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Migrated tool version 1.2 from old tool shed archive to new tool shed repository
author pcingola
date Tue, 07 Jun 2011 17:17:34 -0400
parents 481a95ca5339
children
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481a95ca5339 Migrated tool version 0.9 from old tool shed archive to new tool shed repository
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2 # Interval data is stored here
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3 data_dir = /usr/local/snpEff/data/
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4
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5 # Store cache files here
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6 cache_dir = /tmp
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7
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8 # Comma separated list of genomes
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9 genomes : ce6, danRer6, danRer8_59, dm3, dm5_12, dm5_25_59, hg37, hg37_59, mm37, mm37_59, sacCer2, sacCer59, SIVmac239, testCase, btau4_59, canfam2_59, ggallus_59, chimp2_1_59, rat3_4_59
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11 # For each genome 'XX' a set of attributes are defined:
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12 # - XX.genome : The name of this genome
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13 # - XX.chromosomes : A comma separated list of chromosome names
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14 # - XX.fasta_dir : The directory where fasta files of this genome are located
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15 # - XX.chromo_fasta_files : A comma separated list of the fasta files (one per chromosome).
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16 # WARNING: They must be in the same order as the XX.chromosomes list
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17 #
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18 # Note: Attributes XX.fasta_dir and XX.chromo_fasta_files are only needed if you are building the data
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19 # structures yourself. If you are using a pre-built file, you can leave both of them unassigned.
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20
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21 # Worm (Caenorhabditis elegans), UCSC version 6
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22 ce6.genome : C.Elegans
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23 ce6.chromosomes : I, II, III, IV, V, X, MtDNA
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24 ce6.fasta_dir : ./genomes/ce6/
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25 ce6.chromo_fasta_files : chrI.fa, chrII.fa, chrIII.fa, chrIV.fa, chrV.fa, chrX.fa, chrM.fa
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26 ce6.MtDNA.codonTable : Invertebrate_Mitochondrial
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27
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28 # Zebrafish (Danio rerio), UCSC version 6
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29 danRer6.genome : Danio_rerio
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30 danRer6.chromosomes : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, M
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31 danRer6.fasta_dir : ./genomes/danRer6/
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32 danRer6.chromo_fasta_files : chr1.fa, chr2.fa, chr3.fa, chr4.fa, chr5.fa, chr6.fa, chr7.fa, chr8.fa, chr9.fa, chr10.fa, chr11.fa, chr12.fa, chr13.fa, chr14.fa, chr15.fa, chr16.fa, chr17.fa, chr18.fa, chr19.fa, chr20.fa, chr21.fa, chr22.fa, chr23.fa, chr24.fa, chr25.fa, chrM.fa
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33 danRer6.M.codonTable : Vertebrate_Mitochondrial
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34
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35 # Zebrafish (Danio rerio), ENSEMBL version 8.59
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36 danRer8_59.genome : Danio_rerio
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37 danRer8_59.chromosomes : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, MT
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38 danRer8_59.fasta_dir : ./genomes/danRer8_59/
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39 danRer8_59.chromo_fasta_files : chr1.fa, chr2.fa, chr3.fa, chr4.fa, chr5.fa, chr6.fa, chr7.fa, chr8.fa, chr9.fa, chr10.fa, chr11.fa, chr12.fa, chr13.fa, chr14.fa, chr15.fa, chr16.fa, chr17.fa, chr18.fa, chr19.fa, chr20.fa, chr21.fa, chr22.fa, chr23.fa, chr24.fa, chr25.fa, chrMT.fa
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40 danRer8_59.MT.codonTable : Vertebrate_Mitochondrial
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41
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42 # Fly (D. Melanogaster), UCSC version 3
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43 dm3.genome : D.Melanogaster
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44 dm3.chromosomes : 2L, 2LHet, 2R, 2RHet, 3L, 3LHet, 3R, 3RHet, 4, M, U, X, XHet, YHet
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45 dm3.fasta_dir : ./genomes/dm3/
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46 dm3.chromo_fasta_files : chr2L.fa, chr2LHet.fa, chr2R.fa, chr2RHet.fa, chr3L.fa, chr3LHet.fa, chr3R.fa, chr3RHet.fa, chr4.fa, chrM.fa, chrU.fa, chrX.fa, chrXHet.fa, chrYHet.fa
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47 dm3.M.codonTable : Invertebrate_Mitochondrial
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48
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49 # Fly (D. Melanogaster), ENSEMBL version 5.12
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50 dm5_12.genome : D.Melanogaster
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51 dm5_12.chromosomes : 2L, 2LHet, 2R, 2RHet, 3L, 3LHet, 3R, 3RHet, 4, M, U, X, XHet, YHet
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52 dm5_12.fasta_dir : ./genomes/dm5_12/
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53 dm5_12.chromo_fasta_files : chr2L.fa, chr2LHet.fa, chr2R.fa, chr2RHet.fa, chr3L.fa, chr3LHet.fa, chr3R.fa, chr3RHet.fa, chr4.fa, chrM.fa, chrU.fa, chrX.fa, chrXHet.fa, chrYHet.fa
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54 dm5_12.M.codonTable : Invertebrate_Mitochondrial
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55
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56 # Fly (D. Melanogaster), ENSEMBL version 5.25.59
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57 dm5_25_59.genome : D.Melanogaster
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58 dm5_25_59.chromosomes : 2L, 2LHet, 2R, 2RHet, 3L, 3LHet, 3R, 3RHet, 4, M, U, X, XHet, YHet
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59 dm5_25_59.fasta_dir : ./genomes/dm5_25_59/
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60 dm5_25_59.chromo_fasta_files : chr2L.fa, chr2LHet.fa, chr2R.fa, chr2RHet.fa, chr3L.fa, chr3LHet.fa, chr3R.fa, chr3RHet.fa, chr4.fa, chrM.fa, chrU.fa, chrX.fa, chrXHet.fa, chrYHet.fa
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61 dm5_25_59.M.codonTable : Invertebrate_Mitochondrial
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62
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63 # Human genome, UCSC version hg37
0
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64 hg37.genome : Human
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65 hg37.chromosomes : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y
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66 hg37.fasta_dir : ./genomes/hg37/
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67 hg37.chromo_fasta_files : chr1.fa, chr2.fa, chr3.fa, chr4.fa, chr5.fa, chr6.fa, chr7.fa, chr8.fa, chr9.fa, chr10.fa, chr11.fa, chr12.fa, chr13.fa, chr14.fa, chr15.fa, chr16.fa, chr17.fa, chr18.fa, chr19.fa, chr20.fa, chr21.fa, chr22.fa, chrX.fa, chrY.fa
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68
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69 # Human genome, ENSEMBL version hg37_59
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70 hg37_59.genome : Human
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71 hg37_59.chromosomes : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT
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72 hg37_59.fasta_dir : ./genomes/hg37_59/
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73 hg37_59.chromo_fasta_files : chr1.fa, chr2.fa, chr3.fa, chr4.fa, chr5.fa, chr6.fa, chr7.fa, chr8.fa, chr9.fa, chr10.fa, chr11.fa, chr12.fa, chr13.fa, chr14.fa, chr15.fa, chr16.fa, chr17.fa, chr18.fa, chr19.fa, chr20.fa, chr21.fa, chr22.fa, chrX.fa, chrY.fa, chrMT.fa
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74 hg37_59.MT.codonTable : Vertebrate_Mitochondrial
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75
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76 # Mouse genome, UCSC version mm37
0
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77 mm37.genome : Mouse
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78 mm37.chromosomes : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, X, Y
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79 mm37.fasta_dir : ./genomes/mm37/
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80 mm37.chromo_fasta_files : chr1.fa, chr2.fa, chr3.fa, chr4.fa, chr5.fa, chr6.fa, chr7.fa, chr8.fa, chr9.fa, chr10.fa, chr11.fa, chr12.fa, chr13.fa, chr14.fa, chr15.fa, chr16.fa, chr17.fa, chr18.fa, chr19.fa, chrX.fa, chrY.fa
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82 # Mouse genome, ENSEMBL version mm37.59
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83 mm37_59.genome : Mouse
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84 mm37_59.chromosomes : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, X, Y, MT
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85 mm37_59.fasta_dir : ./genomes/mm37_59/
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86 mm37_59.chromo_fasta_files : chr1.fa, chr2.fa, chr3.fa, chr4.fa, chr5.fa, chr6.fa, chr7.fa, chr8.fa, chr9.fa, chr10.fa, chr11.fa, chr12.fa, chr13.fa, chr14.fa, chr15.fa, chr16.fa, chr17.fa, chr18.fa, chr19.fa, chrX.fa, chrY.fa, chrMT.fa
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87 mm37_59.MT.codonTable : Vertebrate_Mitochondrial
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88
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89 # Yeast (Saccharomyces cerevisiae), UCSC version 2
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90 sacCer2.genome : S.Cerevisiae
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91 sacCer2.chromosomes : 2-micron ,I ,II ,III ,IV ,V ,VI ,VII ,VIII, IX ,X ,XI ,XII ,XIII ,XIV ,XV ,XVI, M
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92 sacCer2.fasta_dir : ./genomes/sacCer2/
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93 sacCer2.chromo_fasta_files : 2micron.fa, chrI.fa, chrII.fa, chrIII.fa, chrIV.fa, chrV.fa, chrVI.fa, chrVII.fa, chrVIII.fa, chrIX.fa, chrX.fa, chrXI.fa, chrXII.fa, chrXIII.fa, chrXIV.fa, chrXV.fa, chrXVI.fa, chrM.fa
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94 sacCer2.M.codonTable : Yeast_Mitochondrial
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95
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96 # Yeast (Saccharomyces cerevisiae), ENSEMBL version 59
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97 sacCer59.genome : S.Cerevisiae
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98 sacCer59.chromosomes : 2-micron ,I ,II ,III ,IV ,V ,VI ,VII ,VIII, IX ,X ,XI ,XII ,XIII ,XIV ,XV ,XVI, M
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99 sacCer59.fasta_dir : ./genomes/sacCer59/
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100 sacCer59.chromo_fasta_files : 2micron.fa, chrI.fa, chrII.fa, chrIII.fa, chrIV.fa, chrV.fa, chrVI.fa, chrVII.fa, chrVIII.fa, chrIX.fa, chrX.fa, chrXI.fa, chrXII.fa, chrXIII.fa, chrXIV.fa, chrXV.fa, chrXVI.fa, chrM.fa
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101 sacCer59.M.codonTable : Yeast_Mitochondrial
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102
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103 # HIV virus (SIVmac239, http://www.ncbi.nlm.nih.gov/nuccore/334647)
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104 SIVmac239.genome : HIV
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105 SIVmac239.chromosomes : 1
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106 SIVmac239.fasta_dir : ./genomes/SIVmac239/
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107 SIVmac239.chromo_fasta_files : chr1.fa
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108 SIVmac239.1.codonTable : Bacterial_and_Plant_Plastid
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109
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110 # Test cases are based on ENSEMBL human genome (version 36_58), chrY
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111 testCase.genome : Human
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112 testCase.chromosomes : Y
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113 testCase.fasta_dir : ./genomes/hg37/
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pcingola
parents: 0
diff changeset
114 testCase.chromo_fasta_files : chrY.fa
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115
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pcingola
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diff changeset
116 # Cow, ENSEML 59
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pcingola
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diff changeset
117 btau4_59.genome : Cow
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pcingola
parents: 0
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118 btau4_59.chromosomes : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, X, MT
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119 btau4_59.fasta_dir : ./genomes/btau4_59/
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120 btau4_59.chromo_fasta_files : chr1.fa, chr2.fa, chr3.fa, chr4.fa, chr5.fa, chr6.fa, chr7.fa, chr8.fa, chr9.fa, chr10.fa, chr11.fa, chr12.fa, chr13.fa, chr14.fa, chr15.fa, chr16.fa, chr17.fa, chr18.fa, chr19.fa, chr20.fa, chr21.fa, chr22.fa, chr23.fa, chr24.fa, chr25.fa, chr26.fa, chr27.fa, chr28.fa, chr29.fa, chrX.fa, chrMT.fa
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pcingola
parents: 0
diff changeset
121 btau4_59.MT.codonTable : Vertebrate_Mitochondrial
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pcingola
parents: 0
diff changeset
122
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pcingola
parents: 0
diff changeset
123 # Dog, ENSEMBL 59
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pcingola
parents: 0
diff changeset
124 canfam2_59.genome : Dog
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pcingola
parents: 0
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125 canfam2_59.chromosomes : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38 X, MT
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
126 canfam2_59.fasta_dir : ./genomes/canfam2_59/
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pcingola
parents: 0
diff changeset
127 canfam2_59.chromo_fasta_files : chr1.fa, chr2.fa, chr3.fa, chr4.fa, chr5.fa, chr6.fa, chr7.fa, chr8.fa, chr9.fa, chr10.fa, chr11.fa, chr12.fa, chr13.fa, chr14.fa, chr15.fa, chr16.fa, chr17.fa, chr18.fa, chr19.fa, chr20.fa, chr21.fa, chr22.fa, chr23.fa, chr24.fa, chr25.fa, chr26.fa, chr27.fa, chr28.fa, chr29.fa, chr30.fa, chr31.fa, chr32.fa, chr33.fa, chr34.fa, chr35.fa, chr36.fa, chr37.fa, chr38.fa, chrX.fa, chrMT.fa
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
128 canfam2_59.MT.codonTable : Vertebrate_Mitochondrial
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pcingola
parents: 0
diff changeset
129
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pcingola
parents: 0
diff changeset
130 # Chicken, ENSEMBL 59
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pcingola
parents: 0
diff changeset
131 ggallus_59.genome : Chcken
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pcingola
parents: 0
diff changeset
132 ggallus_59.chromosomes : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, W, Z, MT
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
133 ggallus_59.fasta_dir : ./genomes/ggallus_59/
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pcingola
parents: 0
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134 ggallus_59.chromo_fasta_files : chr1.fa, chr2.fa, chr3.fa, chr4.fa, chr5.fa, chr6.fa, chr7.fa, chr8.fa, chr9.fa, chr10.fa, chr11.fa, chr12.fa, chr13.fa, chr14.fa, chr15.fa, chr16.fa, chr17.fa, chr18.fa, chr19.fa, chr20.fa, chr21.fa, chr22.fa, chr23.fa, chr24.fa, chr25.fa, chr26.fa, chr27.fa, chr28.fa, chrW.fa, chrZ.fa, chrMT.fa
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
135 ggallus_59.MT.codonTable : Vertebrate_Mitochondrial
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pcingola
parents: 0
diff changeset
136
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pcingola
parents: 0
diff changeset
137 # Chimp, ENSEMBL 59
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pcingola
parents: 0
diff changeset
138 chimp2_1_59.genome : Human
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pcingola
parents: 0
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139 chimp2_1_59.chromosomes : 1, 2a, 2b, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
140 chimp2_1_59.fasta_dir : ./genomes/chimp2_1_59/
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pcingola
parents: 0
diff changeset
141 chimp2_1_59.chromo_fasta_files : chr1.fa, chr2a.fa, chr2b.fa, chr3.fa, chr4.fa, chr5.fa, chr6.fa, chr7.fa, chr8.fa, chr9.fa, chr10.fa, chr11.fa, chr12.fa, chr13.fa, chr14.fa, chr15.fa, chr16.fa, chr17.fa, chr18.fa, chr19.fa, chr20.fa, chr21.fa, chr22.fa, chrX.fa, chrY.fa, chrMT.fa
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
142 chimp2_1_59.MT.codonTable : Vertebrate_Mitochondrial
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pcingola
parents: 0
diff changeset
143
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pcingola
parents: 0
diff changeset
144 # Rat, ENSEMBL 59
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pcingola
parents: 0
diff changeset
145 rat3_4_59.genome : Human
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pcingola
parents: 0
diff changeset
146 rat3_4_59.chromosomes : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, X, MT
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
147 rat3_4_59.fasta_dir : ./genomes/rat3_4_59/
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pcingola
parents: 0
diff changeset
148 rat3_4_59.chromo_fasta_files : chr1.fa, chr2.fa, chr3.fa, chr4.fa, chr5.fa, chr6.fa, chr7.fa, chr8.fa, chr9.fa, chr10.fa, chr11.fa, chr12.fa, chr13.fa, chr14.fa, chr15.fa, chr16.fa, chr17.fa, chr18.fa, chr19.fa, chr20.fa, chrX.fa, chrMT.fa
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
149 rat3_4_59.MT.codonTable : Vertebrate_Mitochondrial
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pcingola
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diff changeset
150
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pcingola
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diff changeset
151 # Codon tables
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pcingola
parents: 0
diff changeset
152 #
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pcingola
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diff changeset
153 # Format: It's a comma separated "codon/aminoAcid[+*]" list
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pcingola
parents: 0
diff changeset
154 # Where 'codon' is in uppper case, aminoAcid is a one letter coce, '+' denotes start codon and '*' denotes stop codon
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pcingola
parents: 0
diff changeset
155 #
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pcingola
parents: 0
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156 # References: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
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pcingola
parents: 0
diff changeset
157 # ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
158 codon.Standard: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
159 codon.Vertebrate_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/*, AGG/*, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
160 codon.Yeast_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/T, CTC/T, CTA/T, CTG/T, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
161 codon.Mold_Mitochondrial: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
162 codon.Protozoan_Mitochondrial: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
163 codon.Coelenterate: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
164 codon.Mitochondrial: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
165 codon.Mycoplasma: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
166 codon.Spiroplasma: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
167 codon.Invertebrate_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
168 codon.Ciliate_Nuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
169 codon.Dasycladacean_Nuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
170 codon.Hexamita_Nuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
171 codon.Echinoderm_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
172 codon.Flatworm_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
173 codon.Euplotid_Nuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/C, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
174 codon.Bacterial_and_Plant_Plastid: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
175 codon.Alternative_Yeast_Nuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/S+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
176 codon.Ascidian_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/G, AGG/G, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
177 codon.Alternative_Flatworm_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Y, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
178 codon.Blepharisma_Macronuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
179 codon.Chlorophycean_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
180 codon.Trematode_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
181 codon.Scenedesmus_obliquus_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/*, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
182 codon.Thraustochytrium_Mitochondrial: TTT/F, TTC/F, TTA/*, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
2cf01e805427 Migrated tool version 1.2 from old tool shed archive to new tool shed repository
pcingola
parents: 0
diff changeset
183