nexus
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**{{nexus.pdf|NEXUS}}**: | **{{nexus.pdf|NEXUS}}**: | ||
\\ Systematic Biology 46: | \\ Systematic Biology 46: | ||
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- | http:// | ||
\\ | \\ | ||
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- | + | ===== format | |
- | + | ||
- | ===== Program | + | |
standard text file | standard text file | ||
- | |||
- | ===== Data type handled ===== | ||
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+ | ===== file format: ===== | ||
+ | * NEXUS files are free-format, | ||
+ | * NEXUS files are for the most part not case-sensitive by default. A big exception is in the matrix command, where (by default) an allele named A is treated as being distinct from a | ||
- | ===== Input Files ===== | + | \\ |
* Comments can be added by enclosing text with brackets: '' | * Comments can be added by enclosing text with brackets: '' | ||
* first line must be: ''# | * first line must be: ''# | ||
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* Blocks: series of commands, beginning with a BEGIN command and ending with an END command: < | * Blocks: series of commands, beginning with a BEGIN command and ending with an END command: < | ||
BEGIN block-name; | BEGIN block-name; | ||
- | command-name token . . . ; | + | command-name token . . . ; |
- | command-name token . . . ; | + | |
- | ... | + | ... |
END; | END; | ||
</ | </ | ||
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* **TAXA:** TAXA block defines taxa and gives them names. The block also establishes the order (numbering) of the taxa. Taxa consist of the entities (biological species, haplotypes, manuscripts, | * **TAXA:** TAXA block defines taxa and gives them names. The block also establishes the order (numbering) of the taxa. Taxa consist of the entities (biological species, haplotypes, manuscripts, | ||
BEGIN TAXA; | BEGIN TAXA; | ||
- | DIMENSIONS NTAX=number-of-taxa; | + | DIMENSIONS NTAX=number-of-taxa; |
- | TAXLABELS taxon-name [taxon-name ...] ; | + | |
END; | END; | ||
</ | </ | ||
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[TRANSPOSE] | [TRANSPOSE] | ||
[INTERLEAVE] | [INTERLEAVE] | ||
- | [ITEMS=([MIN][MAX][MEDIAN][AVERAGE][VARIANCE][STCERROR][SAMPLESIZE][STATES])] | + | [ITEMS=([MIN][MAX][MEDIAN][AVERAGE][VARIANCE][STCERROR][SAMPLESIZE][STATES])] |
- | [STATESFORMAT={STATESPRESENT|INDIVIDUALS|COUNT|FREQUENCY}] | + | [STATESFORMAT={STATESPRESENT|INDIVIDUALS|COUNT|FREQUENCY}] |
[[No]TOKENS] | [[No]TOKENS] | ||
;] | ;] | ||
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;] | ;] | ||
| | ||
+ | END; | ||
+ | </ | ||
+ | BEGIN CHARACTERS; | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | taxon_1 absent red big | ||
+ | taxon_2 absent blue small | ||
+ | taxon_3 present blue small; | ||
END; | END; | ||
</ | </ | ||
- | * UNALIGNED: similar to a CHARACTRS block, but it contains unaligned molecular sequence data. < | + | |
BEGIN UNALIGNED; | BEGIN UNALIGNED; | ||
| | ||
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</ | </ | ||
- | * DISTANCES: contains distance matrices < | + | |
BEGIN DISTANCES; | BEGIN DISTANCES; | ||
| | ||
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</ | </ | ||
- | * DATA: is a CHARACTERS block that includes not only the definition of characters but also the definition of taxa (this block is not recommended) < | + | |
BEGIN DATA; | BEGIN DATA; | ||
| | ||
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</ | </ | ||
- | * SETS: descriptions of collections of objects. These objects include characters, taxa, trees, states, and kinds of changes. In addition, partitions of characters, taxa, and trees can be formed. < | + | |
BEGIN SETS; | BEGIN SETS; | ||
| | ||
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</ | </ | ||
- | * ASSUMPTIONS: | + | |
+ | BEGIN ASSUMPTIONS; | ||
+ | | ||
+ | [POLYTCOUNT={MINSTEPS|MAXSTEPS}] | ||
+ | [GAPMODE={MISSING|NEWSTATE}]; | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | END; | ||
+ | </ | ||
+ | BEGIN ASSUMPTIONS; | ||
+ | | ||
+ | | ||
+ | 0 1 2 3 | ||
+ | . 1 2 3 | ||
+ | 1 . 1 2 | ||
+ | 2 1 . 1 | ||
+ | 3 2 1 .; | ||
+ | | ||
+ | | ||
+ | WTSET * one=2: 1-3 6 11-15, 3: 7 8; | ||
+ | WTSET two=2:4 9, 3:1-3 5; | ||
+ | EXSET nolarval=1-9; | ||
+ | | ||
+ | END; | ||
+ | </ | ||
- | * CODONS: contains information about the genetic code, the regions of DNA and RNA sequences that are protein coding, and the location of triplets coding for amino acids in nucleotide sequences. < | + | |
BEGIN CODONS; | BEGIN CODONS; | ||
| | ||
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</ | </ | ||
- | * **TREES** | + | * **TREES:** stores information about trees < |
- | * NOTES: allows attachment of additional information (text, pictures, etc.) to various objects (trees, taxa, characters, etc.) in the file. | + | BEGIN TREES; |
+ | | ||
+ | | ||
+ | [TREE [*] tree-name= tree-specification; | ||
+ | END; | ||
+ | </ | ||
+ | BEGIN TAXA; | ||
+ | | ||
+ | END; | ||
+ | |||
+ | BEGIN TREES; | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | END; | ||
+ | </ | ||
+ | |||
+ | * **NOTES:** allows attachment of additional information (text, pictures, etc.) to various objects (trees, taxa, characters, etc.) in the file. < | ||
+ | BEGIN NOTES; | ||
+ | [TEXT [TAXON=taxon-set] [CARACTER=character-set] [STATE=state-set] [TREE=tree-set] | ||
+ | SOURCE={INLINE|FILE|RESOURCE}TEXT=text-or-source-description: | ||
+ | | ||
+ | [FORMAT=[PICT|TIFF|EPS|JPEG|GIF}] [ENCODE={NONE|UUENCODE|BINHEX}] | ||
+ | [SOURCE={INLINE|FILE|RESOURCE}PICTURE=picture-or-source-descriptior; | ||
+ | END; | ||
+ | </ | ||
\\ | \\ | ||
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* several of the object definitions follow a particular format: GENETICCODE, | * several of the object definitions follow a particular format: GENETICCODE, | ||
+ | \\ | ||
=== example: === | === example: === | ||
< | < | ||
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===== How to cite ===== | ===== How to cite ===== | ||
+ | Description in Maddison, D. R., D. L. Swofford and W. P. Maddison. 1997. NEXUS: | ||
+ | \\ Systematic Biology 46:590-621. | ||
+ | |||
+ | |||
+ | |||
+ | ===== NCL ===== | ||
+ | [[http:// | ||
+ | |||
+ | NEXUS Class Library (NCL) is an integrated collection of C++ classes designed to allow the user to quickly write a program that reads NEXUS-formatted data files. It also allows easy extension of the NEXUS format to include new blocks of your own design | ||
+ | |||
+ |
nexus.1197448193.txt.gz · Last modified: 2008/07/22 13:30 (external edit)