Difference between revisions of "NEXUS file format"
From Christoph's Personal Wiki
(→Syntactic structure: Added more tables, info., etc.) |
(Added another (simple) example + format) |
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==Syntactic structure== | ==Syntactic structure== | ||
| − | The syntactic structure of a | + | The syntactic structure of a '''NEXUS file''' is as follows: |
<pre> | <pre> | ||
| Line 173: | Line 173: | ||
; Definition list : list of definitions | ; Definition list : list of definitions | ||
| + | |||
| + | ==Example Trees== | ||
| + | |||
| + | Two character state trees and the NEXUS commands that define them. The first tree has an unnamed state. | ||
| + | <pre> | ||
| + | 2 3 4 6 | ||
| + | \ / \ / | ||
| + | \ / \ / | ||
| + | * 3 5 | ||
| + | | | / | ||
| + | | |/ | ||
| + | 1 2 | ||
| + | | | | ||
| + | | | | ||
| + | 0 1 | ||
| + | first second | ||
| + | |||
| + | USERTYPE first (CSTREE) = (((2,3))1)0; | ||
| + | USERTYPE second (CSTREE) = (((4,6)3,5)2)1; | ||
| + | </pre> | ||
==Example NEXUS files== | ==Example NEXUS files== | ||
| Line 201: | Line 221: | ||
</pre> | </pre> | ||
| − | === | + | === Simple example (orginal from paper) === |
| + | <pre> | ||
| + | #NEXUS | ||
| + | BEGIN TAXA; | ||
| + | Dimensions NTax=4; | ||
| + | TaxLabels fish frog snake mouse; | ||
| + | END; | ||
| + | |||
| + | BEGIN CHARACTERS; | ||
| + | Dimensions NChar=20; | ||
| + | Format DataType=DNA; | ||
| + | Matrix | ||
| + | fish ACATA GAGGG TACCT CTAAG | ||
| + | frog ACATA GAGGG TACCT CTAAG | ||
| + | snake ACATA GAGGG TACCT CTAAG | ||
| + | mouse ACATA GAGGG TACCT CTAAG | ||
| + | END; | ||
| + | |||
| + | BEGIN TREES; | ||
| + | Tree best=(fish, (frog, (snake, mouse))); | ||
| + | END; | ||
| + | </pre> | ||
| + | |||
| + | === Complex example (orginial from paper) === | ||
''note: block names in bold (<nowiki><b></nowiki>); commands underlined (<nowiki><u></nowiki>).'' | ''note: block names in bold (<nowiki><b></nowiki>); commands underlined (<nowiki><u></nowiki>).'' | ||
<pre> | <pre> | ||
| Line 250: | Line 293: | ||
===DNA=== | ===DNA=== | ||
<pre> | <pre> | ||
| − | # | + | #NEXUS |
| − | + | BEGIN DATA; | |
| − | + | Dimensions NTax=10 NChar=705; | |
| − | + | Format DataType=DNA Interleave=yes Gap=- Missing=?; | |
| − | + | Matrix | |
| − | Cow | + | Cow ATGGC ATATC CCATA CAACT AGGAT TCCAA GATGC AACAT CACCA ATCAT AGAAG AACTA |
Carp ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTT | Carp ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTT | ||
Chicken ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTC | Chicken ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTC | ||
| Line 387: | Line 430: | ||
Frog AACTGATCTTCATCAATACTA---GAAGCATCACTA------AGA | Frog AACTGATCTTCATCAATACTA---GAAGCATCACTA------AGA | ||
; | ; | ||
| − | + | END; | |
</pre> | </pre> | ||
| Line 451: | Line 494: | ||
* [http://www.molevol.org/camel/projects/nexus/ molevol.org - NEXUS] | * [http://www.molevol.org/camel/projects/nexus/ molevol.org - NEXUS] | ||
* [http://tolweb.org/nexus/ Some NEXUS information] | * [http://tolweb.org/nexus/ Some NEXUS information] | ||
| + | * [http://en.wikipedia.org/wiki/Cladogram Wikipedia article on '''cladogram'''] | ||
[[Category:Academic Research]] | [[Category:Academic Research]] | ||
Revision as of 19:35, 28 December 2005
NEXUS is the file format used by many popular programs like GDA, Paup*, Mesquite, ModelTest, MrBayes, and MacClade. Nexus file names often have a .nxs or .nex extension.
The NEXUS format conveys data organized according to the character state data model, in which the features of operational taxonomic units (OTUs) (e.g., species, individuals, genes, genomes, etc.) are observable states of underlying homologous characters. For instance, in a protein sequence alignment, proteins are the OTUs, alignment columns are characters, and amino acids (or gaps) are states. In evolutionary analysis, it is typical to consider differences as the result of state transitions that take place on branches of a tree, therefore the NEXUS file provides a means to represent a tree (in the standard Newick (a.k.a. New Hampshire) format).
Contents
Syntactic structure
The syntactic structure of a NEXUS file is as follows:
#NEXUS
begin < blockname >;
< command > < argument > [additional argument];
[ < another command with args >; ]
end;
[ < another block with commands > ]
- The syntax for the TREES block is
BEGIN TREES;
[Translate arbitrary-token-used-in-tree-description valid-taxon-name
[, arbitrary-token-used-in-tree-description valid-taxon-name ...];]
[Tree [*] tree-name=tree-specification;]
END;
- Example syntax for a TREES block in a NEXUS file
BEGIN TAXA;
TaxLabels Scarabaeus Drosophila Aranaeus;
END;
BEGIN TREES;
Translate beetle Scarabaeus, fly Drosophila, spider Aranaeus;
Tree tree1 = ((1,2),3);
Tree tree2 = ((beetle,fly),spider);
Tree tree3 = ((Scarabaeus,Drosophila),Aranaeus);
END;
Each of the pre-defined types of public blocks may appear only once. The TAXA block is the only necessary block. There are some restrictions on the ordering of blocks, and on the ordering of commands within a block. Application-specific "private" blocks are also possible. NEXUS keywords are not case-sensitive. Names of BLOCKS in upper case, shown here, are only for mnemonic purposes.
| Some important public blocks | |
|---|---|
| Name | Description |
| TAXA | specifies OTUs in data set |
| CHARACTERS | specifies characters |
| SETS | assigns names to sets of characters or OTUs |
| ASSUMPTIONS | houses assumptions about the data or gives general directions as to how to treat them (e.g., which characters are to be excluded from consideration) |
| CODONS | specifies codons and their genetic codes |
| DATA | equivalent to a CHARACTERS block in which the NewTaxa subcommand is included in the Dimensions command |
| TREES | stores information about trees |
| UNALIGNED | |
| DISTANCES | contains distance matrices |
| SETS | stores sets of objects (characters, states, taxa, etc.) |
source: Maddison et al., 1997
| Some important commands | ||
|---|---|---|
| Name | Block | Description |
| TaxLabels | CHARACTERS | allows specification of the names of the taxa |
| CharLabels | CHARACTERS | label for a character (column) |
| StateLabels | CHARACTERS | label for a state (the type of an instance of a character) |
| CharStateLabels | CHARACTERS | combined label for a character and its states |
| CharSet | SETS | specifies and names a set of characters |
| TaxSet | SETS | give a name to some set of OTUs |
| GeneticCode | CODONS | specify a genetic code |
| CodeSet | CODONS | associate a code with a CharSet or TaxSet |
| Tree | TREES | specify a "Newick tree" |
| CodonPosSet | ||
| StateSet | ||
| ChangeSet | ||
| TreeSet | ||
| CharPartition | define partition of characters | |
| TaxPartition | define partition of taxa | |
| TreePartition | define partition of trees | |
| UserType | ||
| WtSet | specifies the weights of each character (standard object definition command) | |
| TypeSet | specifies the type assigned to each character as used in parsimony analysis | |
| ExSet | specifies which characters are to be excluded from consideration | |
| AncStates | allows specification of ancestral states | |
| Common | ||
| Dimensions | specifies the number of characters. | |
| Format | specifies the format of the data Matrix (a crucial command) | |
| Eliminate | allows specification of a list of characters that are to be excluded from consideration. | |
| Matrix | contains a sequence of taxon names and state information for that taxon | |
source: Maddison et al., 1997
Format subcommands
The following are possible formatting subcommands:
- DataType = { standard | DNA | RNA | nucleotide | protein | continuous }
- RespectCase
- Missing
- Gap
- Symbols
- Equate
- MatchChar
- [No]Labels
- Transpose
- Interleave
- Items
- StatesFormat
- [No]Tokens
NEXUS Objects
Many of the commands in a NEXUS file define objects or specify characteristics about them. All objects can be labeled (given names). Duplicate names should be avoided as should names that differ only in case.
List of currently defined objects:
- taxa
- characters
- states
- trees
- genetic codes
- sets (of taxa, characters, states, classes of changes between states, trees)
- partitions (of taxa, trees, characters)
- weight sets
- types
- type sets
- character exclusion sets
- ancestral states
- codon position sets
- Definition list
- list of definitions
Example Trees
Two character state trees and the NEXUS commands that define them. The first tree has an unnamed state.
2 3 4 6
\ / \ /
\ / \ /
* 3 5
| | /
| |/
1 2
| |
| |
0 1
first second
USERTYPE first (CSTREE) = (((2,3))1)0;
USERTYPE second (CSTREE) = (((4,6)3,5)2)1;
Example NEXUS files
Basic
#NEXUS
BEGIN TAXA;
dimensions ntax=4;
taxlabels A B C D;
END;
BEGIN CHARACTERS;
dimensions nchar=5;
format datatype=protein gap=-;
charlabels 1 2 3 4 Five;
matrix
A MA-LL
B MA-LE
C MEATY
D ME-TE
END;
BEGIN TREES;
tree "basic bush" = ((A:1,B:1):1,(C:1,D:1):1);
END;
Simple example (orginal from paper)
#NEXUS
BEGIN TAXA;
Dimensions NTax=4;
TaxLabels fish frog snake mouse;
END;
BEGIN CHARACTERS;
Dimensions NChar=20;
Format DataType=DNA;
Matrix
fish ACATA GAGGG TACCT CTAAG
frog ACATA GAGGG TACCT CTAAG
snake ACATA GAGGG TACCT CTAAG
mouse ACATA GAGGG TACCT CTAAG
END;
BEGIN TREES;
Tree best=(fish, (frog, (snake, mouse)));
END;
Complex example (orginial from paper)
note: block names in bold (<b>); commands underlined (<u>).
BEGIN <b>TAXA</b>;
<u>DIMENSIONS</u> ntax=26;
<u>TAXLABELS</u> O_volvulus_AAB64227.1 O_volvulus_AAB64226.1 C_elegans_AAF39759.1 C_elegans_AAA83577.1
S_cerevisiae_CAA89634.1 C_albicans_AAC12872.1 S_pombe_CAB57444.1 N_crassa_AAA63780.1 M_musculus_AAA40121.1
C_capitata_AAA57249.1 D_virilis_CAA32060.1 D_erecta_AAF23595.1 D_orena_AAF23594.1 D_teissieri_AAF23599.1
D_yakuba_AAF23598.1 D_melanogaster_AAF50095.1 D_mauritiana_AAF23597.1 D_sechellia_AAF23596.1
D_simulans_CAA33720.1 Z_mays_AAB49913.1 O_sativa_AAC14464.1 O_sativa_AAC14465.1 A_thaliana_AAF99769.1
P_tremuloides_AAD01605.1 A_thaliana_BAB09468.1 A_thaliana_AAD29823.2;
END;
BEGIN <b>CHARACTERS</b>;
<u>DIMENSIONS</u> ntax=26 nchar=30;
<u>FORMAT</u> datatype=protein gap=- missing=?;
<u>CHARLABELS</u> 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112
113 114 115 116 117 118 119 120;
<u>MATRIX</u>
M_musculus_AAA40121.1 QGTIHFEQKASGE--PVVLSGQITGLTE-G
C_capitata_AAA57249.1 KGTVHFEQQDAKS--PVLVTGEVNGLAK-G
N_crassa_AAA63780.1 KGTVIFEQESESA--PTTITYDISGNDPNA
<font color="red">--stuff deleted here--</font>
D_simulans_CAA33720.1 KGTVFFEQESSGT--PVKVSGEVCGLAK-G
S_cerevisiae_CAA89634.1 SGVVKFEQASESE--PTTVSYEIAGNSPNA
S_pombe_CAB57444.1 SGVVTFEQVDQNS--QVSVIVDLVGNDANA;
END;
BEGIN <b>ASSUMPTIONS</b>;
<u>WTSET</u> MySoapWeights (VECTOR) = 1 1 1 1 1 1 1 1 0.83 0.8 0.8 0.8 0.8 0.8 0.71 0.71 1 1 1 1 1 1 1 1
1 1 1 1 1 1;
END;
BEGIN <b>TREES</b>;
<u>TREE</u> "Cu-Zn Superoxide Dismutase" = (((((O_volvulus_AAB64227.1:0.31741,O_volvulus_AAB64226.1:0.13498):
0.20268[1],(C_elegans_AAF39759.1:0.14579,C_elegans_AAA83577.1:0.27311):0.2533[1]):0.12655[0.98],
((S_cerevisiae_CAA89634.1:0.28255,C_albicans_AAC12872.1:0.25631):0.08358[0.91],(S_pombe_CAB57444.1:
0.3159,N_crassa_AAA63780.1:0.1635):0.11954[0.97]):0.17514[1]):0.08988[0.77],(M_musculus_AAA40121.1:
0.49149,(C_capitata_AAA57249.1:0.18945,(D_virilis_CAA32060.1:0.11453,(((D_erecta_AAF23595.1:0.00661,
D_orena_AAF23594.1:0.00769):0.00497[0.92],(D_teissieri_AAF23599.1:0.004,D_yakuba_AAF23598.1:0.01012):
0.0073[0.87]):0.01271[0.88],(((D_melanogaster_AAF50095.1:0.00836,D_mauritiana_AAF23597.1:0.00552):
0.00203[0.28],D_sechellia_AAF23596.1:0.01103):0.00398[0.7],D_simulans_CAA33720.1:0.00595):0.00739[0.75]):
0.11795[1]):0.11754[1]):0.12932[1]):0.10326[1]):0.0712[0.9],(((((Z_mays_AAB49913.1:0.05142,
O_sativa_AAC14464.1:0.09031):0.02799[0.98],O_sativa_AAC14465.1:0.06915):0.05245[0.99],
(A_thaliana_AAF99769.1:0.17064,P_tremuloides_AAD01605.1:0.1075):0.08023[1]):0.08596[1],
A_thaliana_BAB09468.1:0.46052):0.06401[0.75],A_thaliana_AAD29823.2:0.42442):0.14252[0.94]);
END;
DNA
#NEXUS
BEGIN DATA;
Dimensions NTax=10 NChar=705;
Format DataType=DNA Interleave=yes Gap=- Missing=?;
Matrix
Cow ATGGC ATATC CCATA CAACT AGGAT TCCAA GATGC AACAT CACCA ATCAT AGAAG AACTA
Carp ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTT
Chicken ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTC
Human ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTT
Loach ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTT
Mouse ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTA
Rat ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTT
Seal ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTA
Whale ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTC
Frog ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTA
Cow CTTCACTTTCATGACCACACGCTAATAATTGTCTTCTTAATTAGCTCATTAGTACTTTAC
Carp CTTCACTTCCACGACCACGCATTAATAATTGTGCTCCTAATTAGCACTTTAGTTTTATAT
Chicken GTTGAATTCCACGACCACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTAC
Human ATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTAT
Loach CTTCACTTCCATGACCATGCCCTAATAATTGTATTTTTGATTAGCGCCCTAGTACTTTAT
Mouse ATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTAT
Rat ACAAACTTTCATGACCACACCCTAATAATTGTATTCCTCATCAGCTCCCTAGTACTTTAT
Seal CTACACTTCCATGACCACACATTAATAATTGTGTTCCTAATTAGCTCATTAGTACTCTAC
Whale CTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTAC
Frog CTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTAC
Cow ATTATTTCACTAATACTAACGACAAAGCTGACCCATACAAGCACGATAGATGCACAAGAA
Carp ATTATTACTGCAATGGTATCAACTAAACTTACTAATAAATATATTCTAGACTCCCAAGAA
Chicken CTTCTAACTCTTATACTTATAGAAAAACTATCA---TCAAACACCGTAGATGCCCAAGAA
Human GCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAA
Loach GTTATTATTACAACCGTCTCAACAAAACTCACTAACATATATATTTTGGACTCACAAGAA
Mouse ATCATCTCGCTAATATTAACAACAAAACTAACACATACAAGCACAATAGATGCACAAGAA
Rat ATTATTTCACTAATACTAACAACAAAACTAACACACACAAGCACAATAGACGCCCAAGAA
Seal ATTATCTCACTTATACTAACCACGAAACTCACCCACACAAGTACAATAGACGCACAAGAA
Whale ATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAA
Frog ATTATTACTATTATAATAACTACTAAACTAACTAATACAAACCTAATGGACGCACAAGAG
Cow GTAGAGACAATCTGAACCATTCTGCCCGCCATCATCTTAATTCTAATTGCTCTTCCTTCT
Carp ATCGAAATCGTATGAACCATTCTACCAGCCGTCATTTTAGTACTAATCGCCCTGCCCTCC
Chicken GTTGAACTAATCTGAACCATCCTACCCGCTATTGTCCTAGTCCTGCTTGCCCTCCCCTCC
Human ATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCC
Loach ATTGAAATCGTATGAACTGTGCTCCCTGCCCTAATCCTCATTTTAATCGCCCTCCCCTCA
Mouse GTTGAAACCATTTGAACTATTCTACCAGCTGTAATCCTTATCATAATTGCTCTCCCCTCT
Rat GTAGAAACAATTTGAACAATTCTCCCAGCTGTCATTCTTATTCTAATTGCCCTTCCCTCC
Seal GTGGAAACGGTGTGAACGATCCTACCCGCTATCATTTTAATTCTCATTGCCCTACCATCA
Whale GTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCA
Frog ATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCC
Cow TTACGAATTCTATACATAATAGATGAAATCAATAACCCATCTCTTACAGTAAAAACCATA
Carp CTACGCATCCTGTACCTTATAGACGAAATTAACGACCCTCACCTGACAATTAAAGCAATA
Chicken CTCCAAATCCTCTACATAATAGACGAAATCGACGAACCTGATCTCACCCTAAAAGCCATC
Human CTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATT
Loach CTACGAATTCTATATCTTATAGACGAGATTAATGACCCCCACCTAACAATTAAGGCCATG
Mouse CTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATA
Rat CTACGAATTCTATACATAATAGACGAGATTAATAACCCAGTTCTAACAGTAAAAACTATA
Seal TTACGAATCCTCTACATAATGGACGAGATCAATAACCCTTCCTTGACCGTAAAAACTATA
Whale TTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATA
Frog CTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATC
Cow GGACATCAGTGATACTGAAGCTATGAGTATACAGATTATGAGGACTTAAGCTTCGACTCC
Carp GGACACCAATGATACTGAAGTTACGAGTATACAGACTATGAAAATCTAGGATTCGACTCC
Chicken GGACACCAATGATACTGAACCTATGAATACACAGACTTCAAGGACCTCTCATTTGACTCC
Human GGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCC
Loach GGGCACCAATGATACTGAAGCTACGAGTATACTGATTATGAAAACTTAAGTTTTGACTCC
Mouse GGGCACCAATGATACTGAAGCTACGAATATACTGACTATGAAGACCTATGCTTTGATTCA
Rat GGACACCAATGATACTGAAGCTATGAATATACTGACTATGAAGACCTATGCTTTGACTCC
Seal GGACATCAGTGATACTGAAGCTATGAGTACACAGACTACGAAGACCTGAACTTTGACTCA
Whale GGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCC
Frog GGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCT
Cow TACATAATTCCAACATCAGAATTAAAGCCAGGGGAGCTACGACTATTAGAAGTCGATAAT
Carp TATATAGTACCAACCCAAGACCTTGCCCCCGGACAATTCCGACTTCTGGAAACAGACCAC
Chicken TACATAACCCCAACAACAGACCTCCCCCTAGGCCACTTCCGCCTACTAGAAGTCGACCAT
Human TACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAAT
Loach TACATAATCCCCACCCAGGACCTAACCCCTGGACAATTCCGGCTACTAGAGACAGACCAC
Mouse TATATAATCCCAACAAACGACCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAAC
Rat TACATAATCCCAACCAATGACCTAAAACCAGGTGAACTTCGTCTATTAGAAGTTGATAAT
Seal TATATGATCCCCACACAAGAACTAAAGCCCGGAGAACTACGACTGCTAGAAGTAGACAAT
Whale TATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAAC
Frog TATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAAT
Cow CGAGTTGTACTACCAATAGAAATAACAATCCGAATGTTAGTCTCCTCTGAAGACGTATTA
Carp CGAATAGTTGTTCCAATAGAATCCCCAGTCCGTGTCCTAGTATCTGCTGAAGACGTGCTA
Chicken CGCATTGTAATCCCCATAGAATCCCCCATTCGAGTAATCATCACCGCTGATGACGTCCTC
Human CGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTG
Loach CGAATGGTTGTTCCCATAGAATCCCCTATTCGCATTCTTGTTTCCGCCGAAGATGTACTA
Mouse CGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTC
Rat CGGGTAGTCTTACCAATAGAACTTCCAATTCGTATACTAATCTCATCCGAAGACGTCCTG
Seal CGAGTAGTCCTCCCAATAGAAATAACAATCCGCATACTAATCTCATCAGAAGATGTACTC
Whale CGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTC
Frog CGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTC
Cow CACTCATGAGCTGTGCCCTCTCTAGGACTAAAAACAGACGCAATCCCAGGCCGTCTAAAC
Carp CATTCTTGAGCTGTTCCATCCCTTGGCGTAAAAATGGACGCAGTCCCAGGACGACTAAAT
Chicken CACTCATGAGCCGTACCCGCCCTCGGGGTAAAAACAGACGCAATCCCTGGACGACTAAAT
Human CACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAAC
Loach CACTCCTGGGCCCTTCCAGCCATGGGGGTAAAGATAGACGCGGTCCCAGGACGCCTTAAC
Mouse CACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCCAGGCCGACTAAAT
Rat CACTCATGAGCCATCCCTTCACTAGGGTTAAAAACCGACGCAATCCCCGGCCGCCTAAAC
Seal CACTCATGAGCCGTACCGTCCCTAGGACTAAAAACTGATGCTATCCCAGGACGACTAAAC
Whale CACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAAC
Frog CACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCAT
Cow CAAACAACCCTTATATCGTCCCGTCCAGGCTTATATTACGGTCAATGCTCAGAAATTTGC
Carp CAAGCCGCCTTTATTGCCTCACGCCCAGGGGTCTTTTACGGACAATGCTCTGAAATTTGT
Chicken CAAACCTCCTTCATCACCACTCGACCAGGAGTGTTTTACGGACAATGCTCAGAAATCTGC
Human CAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGT
Loach CAAACCGCCTTTATTGCCTCCCGCCCCGGGGTATTCTATGGGCAATGCTCAGAAATCTGT
Mouse CAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGT
Rat CAAGCTACAGTCACATCAAACCGACCAGGTCTATTCTATGGCCAATGCTCTGAAATTTGC
Seal CAAACAACCCTAATAACCATACGACCAGGACTGTACTACGGTCAATGCTCAGAAATCTGT
Whale CAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGC
Frog CAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGC
Cow GGGTCAAACCACAGTTTCATACCCATTGTCCTTGAGTTAGTCCCACTAAAGTACTTTGAA
Carp GGAGCTAATCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCTCTCGAACACTTCGAA
Chicken GGAGCTAACCACAGCTACATACCCATTGTAGTAGAGTCTACCCCCCTAAAACACTTTGAA
Human GGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAA
Loach GGAGCAAACCACAGCTTTATACCCATCGTAGTAGAAGCGGTCCCACTATCTCACTTCGAA
Mouse GGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAA
Rat GGCTCAAATCACAGCTTCATACCCATTGTACTAGAAATAGTGCCTCTAAAATATTTCGAA
Seal GGTTCAAACCACAGCTTCATACCTATTGTCCTCGAATTGGTCCCACTATCCCACTTCGAG
Whale GGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAA
Frog GGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAA
Cow AAATGATCTGCGTCAATATTA---------------------TAA
Carp AACTGATCCTCATTAATACTAGAAGACGCCTCGCTAGGAAGCTAA
Chicken GCCTGATCCTCACTA------------------CTGTCATCTTAA
Human ATA---------------------GGGCCCGTATTTACCCTATAG
Loach AACTGGTCCACCCTTATACTAAAAGACGCCTCACTAGGAAGCTAA
Mouse AACTGATCTGCTTCAATAATT---------------------TAA
Rat AACTGATCAGCTTCTATAATT---------------------TAA
Seal AAATGATCTACCTCAATGCTT---------------------TAA
Whale AAATGATCTGTATCAATACTA---------------------TAA
Frog AACTGATCTTCATCAATACTA---GAAGCATCACTA------AGA
;
END;
Amino Acid
#NEXUS Begin data; Dimensions ntax=10 nchar=234; Format datatype=protein gap=- interleave; Matrix Cow MAYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE Carp MAHPTQLGFKDAAMPVMEELLHFHDHALMIVLLISTLVLYIITAMVSTKLTNKYILDSQE Chicken MANHSQLGFQDASSPIMEELVEFHDHALMVALAICSLVLYLLTLMLMEKLS-SNTVDAQE Human MAHAAQVGLQDATSPIMEELITFHDHALMIIFLICFLVLYALFLTLTTKLTNTNISDAQE Loach MAHPTQLGFQDAASPVMEELLHFHDHALMIVFLISALVLYVIITTVSTKLTNMYILDSQE Mouse MAYPFQLGLQDATSPIMEELMNFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE Rat MAYPFQLGLQDATSPIMEELTNFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE Seal MAYPLQMGLQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE Whale MAYPFQLGFQDAASPIMEELLHFHDHTLMIVFLISSLVLYIITLMLTTKLTHTSTMDAQE Frog MAHPSQLGFQDAASPIMEELLHFHDHTLMAVFLISTLVLYIITIMMTTKLTNTNLMDAQE Cow VETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDS Carp IEIVWTILPAVILVLIALPSLRILYLMDEINDPHLTIKAMGHQWYWSYEYTDYENLGFDS Chicken VELIWTILPAIVLVLLALPSLQILYMMDEIDEPDLTLKAIGHQWYWTYEYTDFKDLSFDS Human METVWTILPAIILVLIALPSLRILYMTDEVNDPSLTIKSIGHQWYWTYEYTDYGGLIFNS Loach IEIVWTVLPALILILIALPSLRILYLMDEINDPHLTIKAMGHQWYWSYEYTDYENLSFDS Mouse VETIWTILPAVILIMIALPSLRILYMMDEINNPVLTVKTMGHQWYWSYEYTDYEDLCFDS Rat VETIWTILPAVILILIALPSLRILYMMDEINNPVLTVKTMGHQWYWSYEYTDYEDLCFDS Seal VETVWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLNFDS Whale VETVWTILPAIILILIALPSLRILYMMDEVNNPSLTVKTMGHQWYWSYEYTDYEDLSFDS Frog IEMVWTIMPAISLIMIALPSLRILYLMDEVNDPHLTIKAIGHQWYWSYEYTNYEDLSFDS Cow YMIPTSELKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLN Carp YMVPTQDLAPGQFRLLETDHRMVVPMESPVRVLVSAEDVLHSWAVPSLGVKMDAVPGRLN Chicken YMTPTTDLPLGHFRLLEVDHRIVIPMESPIRVIITADDVLHSWAVPALGVKTDAIPGRLN Human YMLPPLFLEPGDLRLLDVDNRVVLPIEAPIRMMITSQDVLHSWAVPTLGLKTDAIPGRLN Loach YMIPTQDLTPGQFRLLETDHRMVVPMESPIRILVSAEDVLHSWALPAMGVKMDAVPGRLN Mouse YMIPTNDLKPGELRLLEVDNRVVLPMELPIRMLISSEDVLHSWAVPSLGLKTDAIPGRLN Rat YMIPTNDLKPGELRLLEVDNRVVLPMELPIRMLISSEDVLHSWAIPSLGLKTDAIPGRLN Seal YMIPTQELKPGELRLLEVDNRVVLPMEMTIRMLISSEDVLHSWAVPSLGLKTDAIPGRLN Whale YMIPTSDLKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLN Frog YMIPTNDLTPGQFRLLEVDNRMVVPMESPTRLLVTAEDVLHSWAVPSLGVKTDAIPGRLH Cow QTTLMSSRPGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSASML------- Carp QAAFIASRPGVFYGQCSEICGANHSFMPIVVEAVPLEHFENWSSLMLEDASLGS Chicken QTSFITTRPGVFYGQCSEICGANHSYMPIVVESTPLKHFEAWSSL------LSS Human QTTFTATRPGVYYGQCSEICGANHSFMPIVLELIPLKIFEM-------GPVFTL Loach QTAFIASRPGVFYGQCSEICGANHSFMPIVVEAVPLSHFENWSTLMLKDASLGS Mouse QATVTSNRPGLFYGQCSEICGSNHSFMPIVLEMVPLKYFENWSASMI------- Rat QATVTSNRPGLFYGQCSEICGSNHSFMPIVLEMVPLKYFENWSASMI------- Seal QTTLMTMRPGLYYGQCSEICGSNHSFMPIVLELVPLSHFEKWSTSML------- Whale QTTLMSTRPGLFYGQCSEICGSNHSFMPIVLELVPLEVFEKWSVSML------- Frog QTSFIATRPGVFYGQCSEICGANHSFMPIVVEAVPLTDFENWSSSML-EASL-- ; End;
References
- Maddison DR, Swofford DL, and Maddison WP (1997). NEXUS: An extensible file format for systematic information. Syst. Biol. 46:590-621. (PDF)
