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

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Command FormatCommand Referenceyour data file to be MacClade-compatible, then commands visible toMacClade (i.e., those not contained within a PAUP block) should not beabbreviated.IDENTIFIERS"Identifiers" are simply names given to taxa, characters, and other PAUPinput elements such as character-sets, taxon-sets, and exclusion-sets. Theymay include any combination of upper- and lower-case alphabeticcharacters, digits, and punctuation. If the identifier contains any of thefollowing characters:( ) [ ] { } / \ , ; : = * ' " ` + - < >or a blank, the entire identifier must be enclosed in single quotes.Underscores (_) are translated to blanks, unless the identifier is enclosed insingle quotes. For example, the identifiers Homo_sapiens and'Homo sapiens' are equivalent, but distinct from 'Homo_sapiens'. Toinclude a single-quote in the identifier, you must use two consecutivesingle quotes. Any trailing blanks are stripped before the identifier isstored; leading blanks are preserved.Examples of valid identifiers:subterraneusMus_musculusH._sapiens'H. sapiens #429''Fred''s new sp.''rusticus (1)''"shoal bass"'AMNION_23x21.02myTypePAUP* imposes limits on the lengths of identifiers as defined below. If youuse identifiers that exceed these limits, PAUP* simply truncates them to themaximum acceptable length. If you use names that are longer than themaximum lengths (e.g., for other NEXUS programs that allow longeridentifiers), you should make sure that identifiers in the same class will beunique after truncation by PAUP*.MacClade will not accept all-digit character or taxon names. PAUP* allowsthem, with a warning that taxon/character names have precedence overnumbers (e.g., if the tenth character is named "5", the command EXSET*no_5=5 causes character number five to be excluded by MacClade andcharacter number ten to be excluded by PAUP*). It is not advisable to useall-digit names in PAUP*, especially if you intend to also use the data file inMacClade. (See ALLDIGLAB on page 118 for a description of digit labelhandling.)6 February, 2002 PAUP* 4.0 beta documentation
Command ReferenceCommand FormatTaxon identifiersFor input, taxa may be referenced either by name or by number. Thenumbers are simply the row number of the taxon in the input data matrix.Note that if you delete taxa, the original taxon numbers are still used to referto taxa.The maximum length of a taxon name is 127 characters. However, in mostoutput these names will be truncated to 16 characters due to overall linelengthconstraints. Thus, to avoid confusion you should make the first 16characters of your taxon names unique. The full names will be used ingraphical tree output. If you specify SET TAXLABELS=FULL, then full taxonnames will be used for tree diagrams (but not in other contexts) in normaloutput as well (although they will still be truncated somewhat if the totaloutput width cannot accommodate the long names).Taxon names have priority over taxon numbers in input commands. Thisonly becomes an issue if you use all-digit taxon names. For example, if fivetaxa in a data file are, for whatever reason, given the namesOne34three3673then the command delete 3; would cause deletion of the fourth taxon.Because of the potential confusion, you are strongly urged not to use alldigittaxon names.The name "ALL" is reserved for a taxon list containing all of the taxa in the datamatrix (see below). You may not name a taxon "ALL".Character identifiersOrdinarily, PAUP* refers to characters by consecutive integers starting with1. These integers are used both for input commands and in the output. Youmay also assign alphanumeric character names if you wish. The maximumlength of a character name is 127, but PAUP* truncates character names to10 characters in its output. Thus, you should choose names that are uniqueup to at least the first 10 characters. If you assign alphanumeric characternames, these will also be used to identify characters in PAUP* output.The rules for including punctuation, underscores, and blank characters arethe same for character names as for taxon names (see page 6).As for taxa, character names have priority over character numbers. Forexample, if you used all-digit character names (e.g., sequence positions orrestriction-map locations) such asPAUP* 4.0 beta documentation February, 2002 7
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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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