Masterarbeit, Heidi Lischer

User Tools

Site Tools

Trace: • mega
nexus

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
nexus [2007/12/17 16:21] – heidinexus [2008/07/22 13:31] (current) – external edit 127.0.0.1
Line 12: Line 12:
 ===== format information ===== ===== format information =====
 standard text file standard text file
 +
 +
 +
  
  
Line 25: Line 28:
     * Blocks: series of commands, beginning with a BEGIN command and ending with an END command: <code>     * Blocks: series of commands, beginning with a BEGIN command and ending with an END command: <code>
 BEGIN block-name; BEGIN block-name;
-command-name token . . . ; + command-name token . . . ; 
-command-name token . . . ; + command-name token . . . ; 
-...+ ...
 END; END;
 </code> </code>
Line 34: Line 37:
   * **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, etc.) whose attributes might be recorded in characters and whose relationships are described in trees <code>   * **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, etc.) whose attributes might be recorded in characters and whose relationships are described in trees <code>
 BEGIN TAXA; BEGIN TAXA;
-DIMENSIONS NTAX=number-of-taxa; + DIMENSIONS NTAX=number-of-taxa; 
-TAXLABELS taxon-name [taxon-name ...] ;+ TAXLABELS taxon-name [taxon-name ...] ;
 END; END;
 </code> </code>
Line 52: Line 55:
   [TRANSPOSE]   [TRANSPOSE]
   [INTERLEAVE]   [INTERLEAVE]
-  [ITEMS=([MIN][MAX][MEDIAN][AVERAGE][VARIANCE][STCERROR][SAMPLESIZE][STATES])]   default: STATES +  [ITEMS=([MIN][MAX][MEDIAN][AVERAGE][VARIANCE][STCERROR][SAMPLESIZE][STATES])]  default: STATES 
-  [STATESFORMAT={STATESPRESENT|INDIVIDUALS|COUNT|FREQUENCY}]                      default: STATESPERSENT+  [STATESFORMAT={STATESPRESENT|INDIVIDUALS|COUNT|FREQUENCY}]                     default: STATESPERSENT
   [[No]TOKENS]   [[No]TOKENS]
  ;]  ;]
Line 68: Line 71:
  ;]  ;]
  MATRIX data-matrix;  MATRIX data-matrix;
 +END;
 +</code> example: <code>
 +BEGIN CHARACTERS;
 + DIMENSION NCHAR=3;
 + CHARSTATELABELS 1 hair/absent present, 2 color/red blue, 3 size/small big;
 + FORMAT TOKENS;
 + MATRIX
 +  taxon_1 absent red big
 +  taxon_2 absent blue small
 +  taxon_3 present blue small;
 END; END;
 </code> </code>
  
-  * UNALIGNED: similar to a CHARACTRS block, but it contains unaligned molecular sequence data. <code>+  * **UNALIGNED:** similar to a CHARACTRS block, but it contains unaligned molecular sequence data. <code>
 BEGIN UNALIGNED; BEGIN UNALIGNED;
  [DIMENSIONS NEWTAXA NTAX=number-of-taxa;]  [DIMENSIONS NEWTAXA NTAX=number-of-taxa;]
Line 95: Line 108:
 </code> </code>
  
-  * DISTANCES: contains distance matrices <code>+  * **DISTANCES:** contains distance matrices <code>
 BEGIN DISTANCES; BEGIN DISTANCES;
  [DIMENSIONS [NEWTAXA] NTAX=number-of-taxa NCHAR=number-of-characters;]  [DIMENSIONS [NEWTAXA] NTAX=number-of-taxa NCHAR=number-of-characters;]
Line 118: Line 131:
 </code> </code>
  
-  * DATA: is a CHARACTERS block that includes not only the definition of characters but also the definition of taxa (this block is not recommended) <code>+  * **DATA:** is a CHARACTERS block that includes not only the definition of characters but also the definition of taxa (this block is not recommended) <code>
 BEGIN DATA; BEGIN DATA;
  DIMENSIONS NTAX=5 NCHAR=20;  DIMENSIONS NTAX=5 NCHAR=20;
Line 131: Line 144:
 </code> </code>
  
-  * 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. <code>+  * **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. <code>
 BEGIN SETS; BEGIN SETS;
  [CHARSET charstet_name [({STANDARD|VECTOR})]=character-set;]  [CHARSET charstet_name [({STANDARD|VECTOR})]=character-set;]
Line 157: Line 170:
 </code> </code>
  
-  * ASSUMPTIONS: assumptions about the data. These can include assignment of weights to various characters, specification of the nature of character changes, exclusion of particular characters, and designation of ancestral states. <code>+  * **ASSUMPTIONS:** assumptions about the data. These can include assignment of weights to various characters, specification of the nature of character changes, exclusion of particular characters, and designation of ancestral states. <code>
 BEGIN ASSUMPTIONS; BEGIN ASSUMPTIONS;
  [OPTIONS [DEFTYPE=type-name]  [OPTIONS [DEFTYPE=type-name]
Line 186: Line 199:
 </code> </code>
  
-  * 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. <code>+  * **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. <code>
 BEGIN CODONS; BEGIN CODONS;
  [CODONPOSSET [*] name [({STANDARD|VECTOR})]=  [CODONPOSSET [*] name [({STANDARD|VECTOR})]=
Line 220: Line 233:
 </code> </code>
  
-  * NOTES: allows attachment of additional information (text, pictures, etc.) to various objects (trees, taxa, characters, etc.) in the file. <code>+  * **NOTES:** allows attachment of additional information (text, pictures, etc.) to various objects (trees, taxa, characters, etc.) in the file. <code>
 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]
Line 266: Line 279:
 Description in Maddison, D. R., D. L. Swofford and W. P. Maddison. 1997. NEXUS:  an extensible file format for systematic information.  Description in Maddison, D. R., D. L. Swofford and W. P. Maddison. 1997. NEXUS:  an extensible file format for systematic information. 
 \\ Systematic Biology 46:590-621. \\ Systematic Biology 46:590-621.
 +
  
  
Line 271: Line 285:
 [[http://hydrodictyon.eeb.uconn.edu/ncl/|NCL]] [[http://hydrodictyon.eeb.uconn.edu/ncl/|NCL]]
  
-C++ class library for parsing NEXUS data files  +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.1197904919.txt.gz · Last modified: 2008/07/22 13:30 (external edit)