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Eric Coissac
2024-01-04 14:27:33 +01:00
parent 5b57139450
commit 6fca03227a
20 changed files with 19 additions and 1224962 deletions
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19
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@ -97,3 +97,22 @@ bug_obimultiplex/toto_mapping
bug_obimultiplex/tutu
bug_obimultiplex/tutu_mapping
bug_obipairing/GIT1_GH_ngsfilter.txt
doc/book/TAXO/citations.dmp
doc/book/TAXO/delnodes.dmp
doc/book/TAXO/division.dmp
doc/book/TAXO/gc.prt
doc/book/TAXO/gencode.dmp
doc/book/TAXO/merged.dmp
doc/book/TAXO/names.dmp
doc/book/TAXO/nodes.dmp
doc/book/TAXO/readme.txt
doc/book/wolf_data/Release-253/ncbitaxo/citations.dmp
doc/book/wolf_data/Release-253/ncbitaxo/delnodes.dmp
doc/book/wolf_data/Release-253/ncbitaxo/division.dmp
doc/book/wolf_data/Release-253/ncbitaxo/gc.prt
doc/book/wolf_data/Release-253/ncbitaxo/gencode.dmp
doc/book/wolf_data/Release-253/ncbitaxo/merged.dmp
doc/book/wolf_data/Release-253/ncbitaxo/names.dmp
doc/book/wolf_data/Release-253/ncbitaxo/nodes.dmp
doc/book/wolf_data/Release-253/ncbitaxo/readme.txt
doc/book/results/toto.tasta

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@ -1,12 +0,0 @@
0 | BCT | Bacteria | |
1 | INV | Invertebrates | |
2 | MAM | Mammals | |
3 | PHG | Phages | |
4 | PLN | Plants and Fungi | |
5 | PRI | Primates | |
6 | ROD | Rodents | |
7 | SYN | Synthetic and Chimeric | |
8 | UNA | Unassigned | No species nodes should inherit this division assignment |
9 | VRL | Viruses | |
10 | VRT | Vertebrates | |
11 | ENV | Environmental samples | Anonymous sequences cloned directly from the environment |

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@ -1,358 +0,0 @@
--**************************************************************************
-- This is the NCBI genetic code table
-- Initial base data set from Andrzej Elzanowski while at PIR International
-- Addition of Eubacterial and Alternative Yeast by J.Ostell at NCBI
-- Base 1-3 of each codon have been added as comments to facilitate
-- readability at the suggestion of Peter Rice, EMBL
-- Later additions by Taxonomy Group staff at NCBI
--
-- Version 4.6
-- Renamed genetic code 24 to Rhabdopleuridae Mitochondrial
--
-- Version 4.5
-- Added Cephalodiscidae mitochondrial genetic code 33
--
-- Version 4.4
-- Added GTG as start codon for genetic code 3
-- Added Balanophoraceae plastid genetic code 32
--
-- Version 4.3
-- Change to CTG -> Leu in genetic codes 27, 28, 29, 30
--
-- Version 4.2
-- Added Karyorelict nuclear genetic code 27
-- Added Condylostoma nuclear genetic code 28
-- Added Mesodinium nuclear genetic code 29
-- Added Peritrich nuclear genetic code 30
-- Added Blastocrithidia nuclear genetic code 31
--
-- Version 4.1
-- Added Pachysolen tannophilus nuclear genetic code 26
--
-- Version 4.0
-- Updated version to reflect numerous undocumented changes:
-- Corrected start codons for genetic code 25
-- Name of new genetic code is Candidate Division SR1 and Gracilibacteria
-- Added candidate division SR1 nuclear genetic code 25
-- Added GTG as start codon for genetic code 24
-- Corrected Pterobranchia Mitochondrial genetic code (24)
-- Added genetic code 24, Pterobranchia Mitochondrial
-- Genetic code 11 is now Bacterial, Archaeal and Plant Plastid
-- Fixed capitalization of mitochondrial in codes 22 and 23
-- Added GTG, ATA, and TTG as alternative start codons to code 13
--
-- Version 3.9
-- Code 14 differs from code 9 only by translating UAA to Tyr rather than
-- STOP. A recent study (Telford et al, 2000) has found no evidence that
-- the codon UAA codes for Tyr in the flatworms, but other opinions exist.
-- There are very few GenBank records that are translated with code 14,
-- but a test translation shows that retranslating these records with code
-- 9 can cause premature terminations. Therefore, GenBank will maintain
-- code 14 until further information becomes available.
--
-- Version 3.8
-- Added GTG start to Echinoderm mitochondrial code, code 9
--
-- Version 3.7
-- Added code 23 Thraustochytrium mitochondrial code
-- formerly OGMP code 93
-- submitted by Gertraude Berger, Ph.D.
--
-- Version 3.6
-- Added code 22 TAG-Leu, TCA-stop
-- found in mitochondrial DNA of Scenedesmus obliquus
-- submitted by Gertraude Berger, Ph.D.
-- Organelle Genome Megasequencing Program, Univ Montreal
--
-- Version 3.5
-- Added code 21, Trematode Mitochondrial
-- (as deduced from: Garey & Wolstenholme,1989; Ohama et al, 1990)
-- Added code 16, Chlorophycean Mitochondrial
-- (TAG can translated to Leucine instaed to STOP in chlorophyceans
-- and fungi)
--
-- Version 3.4
-- Added CTG,TTG as allowed alternate start codons in Standard code.
-- Prats et al. 1989, Hann et al. 1992
--
-- Version 3.3 - 10/13/95
-- Added alternate intiation codon ATC to code 5
-- based on complete mitochondrial genome of honeybee
-- Crozier and Crozier (1993)
--
-- Version 3.2 - 6/24/95
-- Code Comments
-- 10 Alternative Ciliate Macronuclear renamed to Euplotid Macro...
-- 15 Blepharisma Macro.. code added
-- 5 Invertebrate Mito.. GTG allowed as alternate initiator
-- 11 Eubacterial renamed to Bacterial as most alternate starts
-- have been found in Archea
--
--
-- Version 3.1 - 1995
-- Updated as per Andrzej Elzanowski at NCBI
-- Complete documentation in NCBI toolkit documentation
-- Note: 2 genetic codes have been deleted
--
-- Old id Use id - Notes
--
-- id 7 id 4 - Kinetoplast code now merged in code id 4
-- id 8 id 1 - all plant chloroplast differences due to RNA edit
--
--
--*************************************************************************
Genetic-code-table ::= {
{
name "Standard" ,
name "SGC0" ,
id 1 ,
ncbieaa "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "---M------**--*----M---------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Vertebrate Mitochondrial" ,
name "SGC1" ,
id 2 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG",
sncbieaa "----------**--------------------MMMM----------**---M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Yeast Mitochondrial" ,
name "SGC2" ,
id 3 ,
ncbieaa "FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "----------**----------------------MM---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate
Mitochondrial; Mycoplasma; Spiroplasma" ,
name "SGC3" ,
id 4 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "--MM------**-------M------------MMMM---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Invertebrate Mitochondrial" ,
name "SGC4" ,
id 5 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG",
sncbieaa "---M------**--------------------MMMM---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear" ,
name "SGC5" ,
id 6 ,
ncbieaa "FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "--------------*--------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Echinoderm Mitochondrial; Flatworm Mitochondrial" ,
name "SGC8" ,
id 9 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
sncbieaa "----------**-----------------------M---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Euplotid Nuclear" ,
name "SGC9" ,
id 10 ,
ncbieaa "FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "----------**-----------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Bacterial, Archaeal and Plant Plastid" ,
id 11 ,
ncbieaa "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "---M------**--*----M------------MMMM---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Alternative Yeast Nuclear" ,
id 12 ,
ncbieaa "FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "----------**--*----M---------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Ascidian Mitochondrial" ,
id 13 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG",
sncbieaa "---M------**----------------------MM---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Alternative Flatworm Mitochondrial" ,
id 14 ,
ncbieaa "FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
sncbieaa "-----------*-----------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Blepharisma Macronuclear" ,
id 15 ,
ncbieaa "FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "----------*---*--------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Chlorophycean Mitochondrial" ,
id 16 ,
ncbieaa "FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "----------*---*--------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Trematode Mitochondrial" ,
id 21 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
sncbieaa "----------**-----------------------M---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Scenedesmus obliquus Mitochondrial" ,
id 22 ,
ncbieaa "FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "------*---*---*--------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Thraustochytrium Mitochondrial" ,
id 23 ,
ncbieaa "FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "--*-------**--*-----------------M--M---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Rhabdopleuridae Mitochondrial" ,
id 24 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG",
sncbieaa "---M------**-------M---------------M---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Candidate Division SR1 and Gracilibacteria" ,
id 25 ,
ncbieaa "FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "---M------**-----------------------M---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Pachysolen tannophilus Nuclear" ,
id 26 ,
ncbieaa "FFLLSSSSYY**CC*WLLLAPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "----------**--*----M---------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Karyorelict Nuclear" ,
id 27 ,
ncbieaa "FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "--------------*--------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Condylostoma Nuclear" ,
id 28 ,
ncbieaa "FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "----------**--*--------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Mesodinium Nuclear" ,
id 29 ,
ncbieaa "FFLLSSSSYYYYCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "--------------*--------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Peritrich Nuclear" ,
id 30 ,
ncbieaa "FFLLSSSSYYEECC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "--------------*--------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Blastocrithidia Nuclear" ,
id 31 ,
ncbieaa "FFLLSSSSYYEECCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "----------**-----------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Balanophoraceae Plastid" ,
id 32 ,
ncbieaa "FFLLSSSSYY*WCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "---M------*---*----M------------MMMM---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Cephalodiscidae Mitochondrial" ,
id 33 ,
ncbieaa "FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG",
sncbieaa "---M-------*-------M---------------M---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
}
}

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doc/book/TAXO/gencode.dmp
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@ -1,28 +0,0 @@
0 | | Unspecified | | |
1 | | Standard | FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ---M------**--*----M---------------M---------------------------- |
2 | | Vertebrate Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG | ----------**--------------------MMMM----------**---M------------ |
3 | | Yeast Mitochondrial | FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**----------------------MM---------------M------------ |
4 | | Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --MM------**-------M------------MMMM---------------M------------ |
5 | | Invertebrate Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG | ---M------**--------------------MMMM---------------M------------ |
6 | | Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear | FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --------------*--------------------M---------------------------- |
9 | | Echinoderm Mitochondrial; Flatworm Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG | ----------**-----------------------M---------------M------------ |
10 | | Euplotid Nuclear | FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**-----------------------M---------------------------- |
11 | | Bacterial, Archaeal and Plant Plastid | FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ---M------**--*----M------------MMMM---------------M------------ |
12 | | Alternative Yeast Nuclear | FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**--*----M---------------M---------------------------- |
13 | | Ascidian Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG | ---M------**----------------------MM---------------M------------ |
14 | | Alternative Flatworm Mitochondrial | FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG | -----------*-----------------------M---------------------------- |
15 | | Blepharisma Macronuclear | FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------*---*--------------------M---------------------------- |
16 | | Chlorophycean Mitochondrial | FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------*---*--------------------M---------------------------- |
21 | | Trematode Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG | ----------**-----------------------M---------------M------------ |
22 | | Scenedesmus obliquus mitochondrial | FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ------*---*---*--------------------M---------------------------- |
23 | | Thraustochytrium mitochondrial code | FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --*-------**--*-----------------M--M---------------M------------ |
24 | | Rhabdopleuridae Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG | ---M------**-------M---------------M---------------M------------ |
25 | | Candidate Division SR1 and Gracilibacteria | FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ---M------**-----------------------M---------------M------------ |
26 | | Pachysolen tannophilus Nuclear | FFLLSSSSYY**CC*WLLLAPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**--*----M---------------M---------------------------- |
27 | | Karyorelict Nuclear | FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --------------*--------------------M---------------------------- |
28 | | Condylostoma Nuclear | FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**--*--------------------M---------------------------- |
29 | | Mesodinium Nuclear | FFLLSSSSYYYYCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --------------*--------------------M---------------------------- |
30 | | Peritrich Nuclear | FFLLSSSSYYEECC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --------------*--------------------M---------------------------- |
31 | | Blastocrithidia Nuclear | FFLLSSSSYYEECCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**-----------------------M---------------------------- |
32 | | Balanophoraceae Plastid | FFLLSSSSYY*WCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ---M------*---*----M------------MMMM---------------M------------ |
33 | | Cephalodiscidae Mitochondrial | FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG | ---M-------*-------M---------------M---------------M------------ |

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*.dmp files are bcp-like dump from GenBank taxonomy database.
General information.
Field terminator is "\t|\t"
Row terminator is "\t|\n"
nodes.dmp file consists of taxonomy nodes. The description for each node includes the following
fields:
tax_id -- node id in GenBank taxonomy database
parent tax_id -- parent node id in GenBank taxonomy database
rank -- rank of this node (superkingdom, kingdom, ...)
embl code -- locus-name prefix; not unique
division id -- see division.dmp file
inherited div flag (1 or 0) -- 1 if node inherits division from parent
genetic code id -- see gencode.dmp file
inherited GC flag (1 or 0) -- 1 if node inherits genetic code from parent
mitochondrial genetic code id -- see gencode.dmp file
inherited MGC flag (1 or 0) -- 1 if node inherits mitochondrial gencode from parent
GenBank hidden flag (1 or 0) -- 1 if name is suppressed in GenBank entry lineage
hidden subtree root flag (1 or 0) -- 1 if this subtree has no sequence data yet
comments -- free-text comments and citations
Taxonomy names file (names.dmp):
tax_id -- the id of node associated with this name
name_txt -- name itself
unique name -- the unique variant of this name if name not unique
name class -- (synonym, common name, ...)
Divisions file (division.dmp):
division id -- taxonomy database division id
division cde -- GenBank division code (three characters)
division name -- e.g. BCT, PLN, VRT, MAM, PRI...
comments
Genetic codes file (gencode.dmp):
genetic code id -- GenBank genetic code id
abbreviation -- genetic code name abbreviation
name -- genetic code name
cde -- translation table for this genetic code
starts -- start codons for this genetic code
Deleted nodes file (delnodes.dmp):
tax_id -- deleted node id
Merged nodes file (merged.dmp):
old_tax_id -- id of nodes which has been merged
new_tax_id -- id of nodes which is result of merging
Citations file (citations.dmp):
cit_id -- the unique id of citation
cit_key -- citation key
pubmed_id -- unique id in PubMed database (0 if not in PubMed)
medline_id -- unique id in MedLine database (0 if not in MedLine)
url -- URL associated with citation
text -- any text (usually article name and authors).
-- The following characters are escaped in this text by a backslash:
-- newline (appear as "\n"),
-- tab character ("\t"),
-- double quotes ('\"'),
-- backslash character ("\\").
taxid_list -- list of node ids separated by a single space

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0 | BCT | Bacteria | |
1 | INV | Invertebrates | |
2 | MAM | Mammals | |
3 | PHG | Phages | |
4 | PLN | Plants and Fungi | |
5 | PRI | Primates | |
6 | ROD | Rodents | |
7 | SYN | Synthetic and Chimeric | |
8 | UNA | Unassigned | No species nodes should inherit this division assignment |
9 | VRL | Viruses | |
10 | VRT | Vertebrates | |
11 | ENV | Environmental samples | Anonymous sequences cloned directly from the environment |

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--**************************************************************************
-- This is the NCBI genetic code table
-- Initial base data set from Andrzej Elzanowski while at PIR International
-- Addition of Eubacterial and Alternative Yeast by J.Ostell at NCBI
-- Base 1-3 of each codon have been added as comments to facilitate
-- readability at the suggestion of Peter Rice, EMBL
-- Later additions by Taxonomy Group staff at NCBI
--
-- Version 4.6
-- Renamed genetic code 24 to Rhabdopleuridae Mitochondrial
--
-- Version 4.5
-- Added Cephalodiscidae mitochondrial genetic code 33
--
-- Version 4.4
-- Added GTG as start codon for genetic code 3
-- Added Balanophoraceae plastid genetic code 32
--
-- Version 4.3
-- Change to CTG -> Leu in genetic codes 27, 28, 29, 30
--
-- Version 4.2
-- Added Karyorelict nuclear genetic code 27
-- Added Condylostoma nuclear genetic code 28
-- Added Mesodinium nuclear genetic code 29
-- Added Peritrich nuclear genetic code 30
-- Added Blastocrithidia nuclear genetic code 31
--
-- Version 4.1
-- Added Pachysolen tannophilus nuclear genetic code 26
--
-- Version 4.0
-- Updated version to reflect numerous undocumented changes:
-- Corrected start codons for genetic code 25
-- Name of new genetic code is Candidate Division SR1 and Gracilibacteria
-- Added candidate division SR1 nuclear genetic code 25
-- Added GTG as start codon for genetic code 24
-- Corrected Pterobranchia Mitochondrial genetic code (24)
-- Added genetic code 24, Pterobranchia Mitochondrial
-- Genetic code 11 is now Bacterial, Archaeal and Plant Plastid
-- Fixed capitalization of mitochondrial in codes 22 and 23
-- Added GTG, ATA, and TTG as alternative start codons to code 13
--
-- Version 3.9
-- Code 14 differs from code 9 only by translating UAA to Tyr rather than
-- STOP. A recent study (Telford et al, 2000) has found no evidence that
-- the codon UAA codes for Tyr in the flatworms, but other opinions exist.
-- There are very few GenBank records that are translated with code 14,
-- but a test translation shows that retranslating these records with code
-- 9 can cause premature terminations. Therefore, GenBank will maintain
-- code 14 until further information becomes available.
--
-- Version 3.8
-- Added GTG start to Echinoderm mitochondrial code, code 9
--
-- Version 3.7
-- Added code 23 Thraustochytrium mitochondrial code
-- formerly OGMP code 93
-- submitted by Gertraude Berger, Ph.D.
--
-- Version 3.6
-- Added code 22 TAG-Leu, TCA-stop
-- found in mitochondrial DNA of Scenedesmus obliquus
-- submitted by Gertraude Berger, Ph.D.
-- Organelle Genome Megasequencing Program, Univ Montreal
--
-- Version 3.5
-- Added code 21, Trematode Mitochondrial
-- (as deduced from: Garey & Wolstenholme,1989; Ohama et al, 1990)
-- Added code 16, Chlorophycean Mitochondrial
-- (TAG can translated to Leucine instaed to STOP in chlorophyceans
-- and fungi)
--
-- Version 3.4
-- Added CTG,TTG as allowed alternate start codons in Standard code.
-- Prats et al. 1989, Hann et al. 1992
--
-- Version 3.3 - 10/13/95
-- Added alternate intiation codon ATC to code 5
-- based on complete mitochondrial genome of honeybee
-- Crozier and Crozier (1993)
--
-- Version 3.2 - 6/24/95
-- Code Comments
-- 10 Alternative Ciliate Macronuclear renamed to Euplotid Macro...
-- 15 Blepharisma Macro.. code added
-- 5 Invertebrate Mito.. GTG allowed as alternate initiator
-- 11 Eubacterial renamed to Bacterial as most alternate starts
-- have been found in Archea
--
--
-- Version 3.1 - 1995
-- Updated as per Andrzej Elzanowski at NCBI
-- Complete documentation in NCBI toolkit documentation
-- Note: 2 genetic codes have been deleted
--
-- Old id Use id - Notes
--
-- id 7 id 4 - Kinetoplast code now merged in code id 4
-- id 8 id 1 - all plant chloroplast differences due to RNA edit
--
--
--*************************************************************************
Genetic-code-table ::= {
{
name "Standard" ,
name "SGC0" ,
id 1 ,
ncbieaa "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "---M------**--*----M---------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Vertebrate Mitochondrial" ,
name "SGC1" ,
id 2 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG",
sncbieaa "----------**--------------------MMMM----------**---M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Yeast Mitochondrial" ,
name "SGC2" ,
id 3 ,
ncbieaa "FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "----------**----------------------MM---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate
Mitochondrial; Mycoplasma; Spiroplasma" ,
name "SGC3" ,
id 4 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "--MM------**-------M------------MMMM---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Invertebrate Mitochondrial" ,
name "SGC4" ,
id 5 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG",
sncbieaa "---M------**--------------------MMMM---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear" ,
name "SGC5" ,
id 6 ,
ncbieaa "FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "--------------*--------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Echinoderm Mitochondrial; Flatworm Mitochondrial" ,
name "SGC8" ,
id 9 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
sncbieaa "----------**-----------------------M---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Euplotid Nuclear" ,
name "SGC9" ,
id 10 ,
ncbieaa "FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "----------**-----------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Bacterial, Archaeal and Plant Plastid" ,
id 11 ,
ncbieaa "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "---M------**--*----M------------MMMM---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Alternative Yeast Nuclear" ,
id 12 ,
ncbieaa "FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "----------**--*----M---------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Ascidian Mitochondrial" ,
id 13 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG",
sncbieaa "---M------**----------------------MM---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Alternative Flatworm Mitochondrial" ,
id 14 ,
ncbieaa "FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
sncbieaa "-----------*-----------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Blepharisma Macronuclear" ,
id 15 ,
ncbieaa "FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "----------*---*--------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Chlorophycean Mitochondrial" ,
id 16 ,
ncbieaa "FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "----------*---*--------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Trematode Mitochondrial" ,
id 21 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
sncbieaa "----------**-----------------------M---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Scenedesmus obliquus Mitochondrial" ,
id 22 ,
ncbieaa "FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "------*---*---*--------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Thraustochytrium Mitochondrial" ,
id 23 ,
ncbieaa "FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "--*-------**--*-----------------M--M---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Rhabdopleuridae Mitochondrial" ,
id 24 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG",
sncbieaa "---M------**-------M---------------M---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Candidate Division SR1 and Gracilibacteria" ,
id 25 ,
ncbieaa "FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "---M------**-----------------------M---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Pachysolen tannophilus Nuclear" ,
id 26 ,
ncbieaa "FFLLSSSSYY**CC*WLLLAPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "----------**--*----M---------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Karyorelict Nuclear" ,
id 27 ,
ncbieaa "FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "--------------*--------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Condylostoma Nuclear" ,
id 28 ,
ncbieaa "FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "----------**--*--------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Mesodinium Nuclear" ,
id 29 ,
ncbieaa "FFLLSSSSYYYYCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "--------------*--------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Peritrich Nuclear" ,
id 30 ,
ncbieaa "FFLLSSSSYYEECC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "--------------*--------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Blastocrithidia Nuclear" ,
id 31 ,
ncbieaa "FFLLSSSSYYEECCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "----------**-----------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Balanophoraceae Plastid" ,
id 32 ,
ncbieaa "FFLLSSSSYY*WCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "---M------*---*----M------------MMMM---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Cephalodiscidae Mitochondrial" ,
id 33 ,
ncbieaa "FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG",
sncbieaa "---M-------*-------M---------------M---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
}
}

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@ -1,28 +0,0 @@
0 | | Unspecified | | |
1 | | Standard | FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ---M------**--*----M---------------M---------------------------- |
2 | | Vertebrate Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG | ----------**--------------------MMMM----------**---M------------ |
3 | | Yeast Mitochondrial | FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**----------------------MM---------------M------------ |
4 | | Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --MM------**-------M------------MMMM---------------M------------ |
5 | | Invertebrate Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG | ---M------**--------------------MMMM---------------M------------ |
6 | | Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear | FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --------------*--------------------M---------------------------- |
9 | | Echinoderm Mitochondrial; Flatworm Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG | ----------**-----------------------M---------------M------------ |
10 | | Euplotid Nuclear | FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**-----------------------M---------------------------- |
11 | | Bacterial, Archaeal and Plant Plastid | FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ---M------**--*----M------------MMMM---------------M------------ |
12 | | Alternative Yeast Nuclear | FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**--*----M---------------M---------------------------- |
13 | | Ascidian Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG | ---M------**----------------------MM---------------M------------ |
14 | | Alternative Flatworm Mitochondrial | FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG | -----------*-----------------------M---------------------------- |
15 | | Blepharisma Macronuclear | FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------*---*--------------------M---------------------------- |
16 | | Chlorophycean Mitochondrial | FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------*---*--------------------M---------------------------- |
21 | | Trematode Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG | ----------**-----------------------M---------------M------------ |
22 | | Scenedesmus obliquus mitochondrial | FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ------*---*---*--------------------M---------------------------- |
23 | | Thraustochytrium mitochondrial code | FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --*-------**--*-----------------M--M---------------M------------ |
24 | | Rhabdopleuridae Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG | ---M------**-------M---------------M---------------M------------ |
25 | | Candidate Division SR1 and Gracilibacteria | FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ---M------**-----------------------M---------------M------------ |
26 | | Pachysolen tannophilus Nuclear | FFLLSSSSYY**CC*WLLLAPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**--*----M---------------M---------------------------- |
27 | | Karyorelict Nuclear | FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --------------*--------------------M---------------------------- |
28 | | Condylostoma Nuclear | FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**--*--------------------M---------------------------- |
29 | | Mesodinium Nuclear | FFLLSSSSYYYYCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --------------*--------------------M---------------------------- |
30 | | Peritrich Nuclear | FFLLSSSSYYEECC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --------------*--------------------M---------------------------- |
31 | | Blastocrithidia Nuclear | FFLLSSSSYYEECCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**-----------------------M---------------------------- |
32 | | Balanophoraceae Plastid | FFLLSSSSYY*WCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ---M------*---*----M------------MMMM---------------M------------ |
33 | | Cephalodiscidae Mitochondrial | FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG | ---M-------*-------M---------------M---------------M------------ |

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*.dmp files are bcp-like dump from GenBank taxonomy database.
General information.
Field terminator is "\t|\t"
Row terminator is "\t|\n"
nodes.dmp file consists of taxonomy nodes. The description for each node includes the following
fields:
tax_id -- node id in GenBank taxonomy database
parent tax_id -- parent node id in GenBank taxonomy database
rank -- rank of this node (superkingdom, kingdom, ...)
embl code -- locus-name prefix; not unique
division id -- see division.dmp file
inherited div flag (1 or 0) -- 1 if node inherits division from parent
genetic code id -- see gencode.dmp file
inherited GC flag (1 or 0) -- 1 if node inherits genetic code from parent
mitochondrial genetic code id -- see gencode.dmp file
inherited MGC flag (1 or 0) -- 1 if node inherits mitochondrial gencode from parent
GenBank hidden flag (1 or 0) -- 1 if name is suppressed in GenBank entry lineage
hidden subtree root flag (1 or 0) -- 1 if this subtree has no sequence data yet
comments -- free-text comments and citations
Taxonomy names file (names.dmp):
tax_id -- the id of node associated with this name
name_txt -- name itself
unique name -- the unique variant of this name if name not unique
name class -- (synonym, common name, ...)
Divisions file (division.dmp):
division id -- taxonomy database division id
division cde -- GenBank division code (three characters)
division name -- e.g. BCT, PLN, VRT, MAM, PRI...
comments
Genetic codes file (gencode.dmp):
genetic code id -- GenBank genetic code id
abbreviation -- genetic code name abbreviation
name -- genetic code name
cde -- translation table for this genetic code
starts -- start codons for this genetic code
Deleted nodes file (delnodes.dmp):
tax_id -- deleted node id
Merged nodes file (merged.dmp):
old_tax_id -- id of nodes which has been merged
new_tax_id -- id of nodes which is result of merging
Citations file (citations.dmp):
cit_id -- the unique id of citation
cit_key -- citation key
pubmed_id -- unique id in PubMed database (0 if not in PubMed)
medline_id -- unique id in MedLine database (0 if not in MedLine)
url -- URL associated with citation
text -- any text (usually article name and authors).
-- The following characters are escaped in this text by a backslash:
-- newline (appear as "\n"),
-- tab character ("\t"),
-- double quotes ('\"'),
-- backslash character ("\\").
taxid_list -- list of node ids separated by a single space