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

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Commands used in the SETS BlockCommand ReferenceTAXSETThis command defines a set of taxa. A TAXSET name can be used insubsequent TAXSET definitions or wherever a taxon-set is required. Thename of a TAXSET cannot be equivalent to a taxon name or taxon number.The taxa to be included are described in a taxon-set. For example, thefollowing commandtaxset beetles = Omma-.;defines the TAXSET "beetles" to include all taxa from taxon Omma to the lastdefined taxon.The VECTOR format consists of 0's and 1's: a 1 indicates that the taxon is tobe included in the TAXSET; whitespace is not necessary between 0's and 1's.CHARPARTITION, TAXPARTITIONThe partition divides the objects into several (mutually exclusive) subsets.They follow the same format, and will be described together.There are several formatting options. The VECTOR format consists of a list ofpartition names. By default, the name of each subset is a NEXUS word (thisis the TOKENS option). The NOTOKENS option is only available in theVECTOR format; this allows one to use single symbols for the subset names.Each value in a definition in VECTOR format must be separated bywhitespace if the names are tokens, but not if they are NOTOKENS.Example 1The following two examples are equivalent:taxpartition populations=1:1-3, 2:4-6, 3:7 8;taxpartition populations (vector notokens) = 11122233;Example 2The following two examples are equivalent:taxpartition mypartition=Chiricahua: 1-3,Huachuca: 4-6, Galiuro: 7 8;taxpartition mypartition (vector) = ChiricahuaChiricahua Chiricahua Huachuca Huachuca HuachucaGaliuro Galiuro;24 February, 2002 PAUP* 4.0 beta documentation
Command ReferenceCommands used in the TREES BlockExample 3The following example of the CHARPARTITION command creates a characterpartition named gfunc which defines coding and noncoding regions of thesequences.charpartition gfunc = 1:2-457 660-896, 2:1 458-659897-898;Example 4The following example of the CHARPARTITION command is equivalent tothe Example 3 except that two predefined character sets are used to definethe characters included in each partition. See the "CharSet" commanddescribed on page 23 for a complete list of predefined character sets.charset coding = 2-457 660-896;charset noncoding = 1 458-659 897-898;charpartition gfunc = 1:coding, 2:noncoding;Commands used in the TREES BlockThe TREES block is used to input user-defined trees to PAUP*. A singleTREE command is used for each tree; any number of TREE commands maybe included in the block.The syntax for the TREES block follows:BEGIN TREES [ block-name ] ;[ TRANSLATE token taxon-name [ , token taxon-name ] … ; ][ TREE [*] name = tree-specification; ]END;TRANSLATEUse the TRANSLATE command to define mappings of arbitrary tokensappearing in the TREE command to valid taxon names. Ordinarily, thetokens are the integers 1 through NTAX. The tree description requiresreferences to the taxa defined in a TAXA, CHARACTERS , DATA, or DISTANCESblock.TREEUse the TREE command to define trees. If no rooting-specification issupplied, the default in PAUP* is to interpret the tree description asspecifying a rooted tree. You can override this behavior by using a "specialcomment." The comment ’[&U]’ indicates that the tree should bePAUP* 4.0 beta documentation February, 2002 25
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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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