nexus
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nexus [2007/12/13 10:09] – heidi | nexus [2008/07/22 13:31] (current) – external edit 127.0.0.1 | ||
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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; | BEGIN ASSUMPTIONS; | ||
| | ||
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</ | </ | ||
- | * 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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</ | </ | ||
- | * NOTES: allows attachment of additional information (text, pictures, etc.) to various objects (trees, taxa, characters, etc.) in the file. < | + | |
BEGIN NOTES; | BEGIN NOTES; | ||
[TEXT [TAXON=taxon-set] [CARACTER=character-set] [STATE=state-set] [TREE=tree-set] | [TEXT [TAXON=taxon-set] [CARACTER=character-set] [STATE=state-set] [TREE=tree-set] | ||
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Description in Maddison, D. R., D. L. Swofford and W. P. Maddison. 1997. NEXUS: | Description in Maddison, D. R., D. L. Swofford and W. P. Maddison. 1997. NEXUS: | ||
\\ Systematic Biology 46:590-621. | \\ 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.1197536941.txt.gz · Last modified: 2008/07/22 13:30 (external edit)