PAUP* 4.0 Beta: Command Reference --Draft Version 3--

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Commands used in the TAXA BlockCommand ReferenceWindow95/NTUNIX’C:\Tree Folder\treefile.trees’/home/users/Bob/tree_folder/treefile.treesUnlike the PAUP* convention for identifiers, underscores (_) are nottranslated into blanks. File-names containing blanks must be enclosedwithin single-quotes for the Macintosh and Window95/NT releases and arenot allowed under either the DOS or Unix releases. See your operatingsystem documentation for other file naming conventions.Commands used in the TAXA BlockThe TAXA block specifies information about taxa. In previous versions ofPAUP, both the taxa information and the character matrix were containedin the DATA block. However, in some instances the character matrix is notneeded, making the option to input only taxa labels useful. While it is stillpermitted, we strongly recommend against use of a DATA block ordefinition of taxa in a CHARACTERS or DISTANCES block because this willprevent some programs from extracting taxon information from the file.BEGIN TAXA;DIMENSIONS NTAX=number-of-taxa;TAXLABELS taxon-name taxon-name ...;END;DIMENSIONS must appear before TAXLABELS, and only one of eachcommand is allowed per block.DIMENSIONSThe DIMENSIONS command specifies the size of the data matrix. The syntaxis:DIMENSIONS NTAX = number-of-taxawhere number-of-taxa and are integer values.TAXLABELSThe TAXLABELS command defines taxa, specifies their names, anddetermines their order. The syntax is:TAXLABELS taxon-name1 taxon-name2 … taxon-name NTAX ;See "Taxon identifiers" on page 7 for rules on the format of taxon names.10 February, 2002 PAUP* 4.0 beta documentation
Command ReferenceCommands used in the CHARACTERS BlockTaxa may also be defined in the CHARACTERS and DISTANCES blocks, if theNEWTAXA token is included in the DIMENSIONS command; see thedescriptions of those blocks for details.Commands used in the CHARACTERS BlockA CHARACTERS block contains the data matrix and other associatedinformation. Taxa are usually not defined in a CHARACTERS block; if they arenot defined here, this block must be preceded by a block which definestaxon labels and ordering (e.g., TAXA). The syntax is:BEGIN CHARACTERS;DIMENSIONS[ NEWTAXA NTAX=number-of-taxa ]NCHAR = number-of-characters;[ FORMAT[ DATATYPE = { STANDARD | DNA | RNA | NUCLEOTIDE |PROTEIN } ][ RESPECTCASE ][ MISSING = symbol ][ GAP = symbol ][ SYMBOLS = "symbol symbol..." ][ EQUATE = "symbol=entry [ symbol=entry... ]" ][ MATCHCHAR = symbol ][ LABELS = { NO | LEFT | RIGHT } ][ TRANSPOSE ][ INTERLEAVE ][ [NO]TOKENS ]; ][ ELIMINATE character-set; ][ TAXLABELS taxon-name taxon-name...; ][ CHARSTATELABELScharacter-number [ character-name ][ /state-name [ state-name... ] ], ...; ][ CHARLABELS character-name [character-name... ]; ][ STATELABELS character-number [ state-name [ state-name... ] ],...; ]MATRIX data-matrix;END;DIMENSIONS, FORMAT, and ELIMINATE must all precede CHARLABELS,STATELABELS, and MATRIX. DIMENSIONS must precede ELIMINATE. Onlyone of each command is allowed per block.DIMENSIONSThe DIMENSIONS command specifies the size of the data matrix. Ordinarily,the CHARACTERS block is proceeded by a TAXA block which contains taxainformation. However, if new taxa are to be defined in the CHARACTERSblock, this must be indicated by the NEWTAXA subcommand. NEWTAXA, ifpresent, must appear before the NTAX subcommand. The numberfollowing NCHAR is the number of characters in the data matrix.PAUP* 4.0 beta documentation February, 2002 11
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ReferencesREFERENCESAdams, E. N., I
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ReferencesHarary, F. 1969. Graph Th
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Referencesdistics 1:186-189.Nei, M.
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PAUP* 4.0 Beta: Command Reference --Draft Version 3--

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