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

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Commands used in the PAUP BlockCommand ReferenceAvailable options• ALL = NO|SETS|TREES|BOTH• SHOWTREE = YES|NO• TREEFILE = tree-file-name• *REPLACE = YES|NO• *APPEND = YES|NO• TCOMPRESS = YES|NO*Option is nonpersistentDescription of optionsALL = NO|SETS|TREES|BOTHUse ALL to calculate agreement subtrees for the trees specified in theAGREE [tree-list]. If ALL = SETS, a list of the agreement sets and thetaxa included within each set is given. If ALL = TREES, all of theagreement subtrees are printed, overriding SHOWTREE = NO if thisoption was specified.SHOWTREE = YES|NOShows the agreement subtree(s) given in the [tree-list].TREEFILE = tree-file-nameIf TREEFILE is specified, a description of all agreement subtrees isoutput to a file containing a NEXUS-format TREES block. Thisoption is not persistent; you must specify it on every AGREEcommand for which you want a tree file to be saved. See "Input/Output files" on page 9 for instructions to specify the full path nameof a file.The following options apply only if FILE is specifiedREPLACE = YES|NOAPPEND = YES|NOIf the specified file already exists, you will be prompted forconfirmation that the existing file should be replaced. Explicitspecification of REPLACE suppresses this prompt; the existingfile will be quietly overwritten by the new data.Alternatively, you may specify APPEND, in which case a newTREES block will be concatenated to the end of an existing file.TCOMPRESS = YES|NOSee "Tree output options" on page 32.34 February, 2002 PAUP* 4.0 beta documentation
Command ReferenceCommands used in the PAUP BlockALLTREESUse the ALLTREES command to perform an exhaustive search of all possibletree topologies.SyntaxALLTREES [options];Menu EquivalentAnalysis > Exhaustive Search ...Available options• KEEP = real-value|NO• ENFORCE = YES|NO• CONSTRAINTS = constraint-name• CONVERSE = YES|NO• FD = NO|BARCHART|HISTOGRAM• NCLASSES = integer-value• FDFILE = frequency-distribution-file-name• SCOREFILE = file-name-for-scores• *REPLACE = YES|NO• STATUS = YES|NO• DSTATUS = integer-value|NONE*Option is nonpersistentDescription of optionsFD = NO|BARCHART|HISTOGRAMUnless FD = NO is specified, a frequency distribution of tree scores isoutput. (Normally, obtaining the frequency distribution is the onlyreason for doing an exhaustive rather than branch-and-boundsearch, so you will probably never specify this option.) FD =BARCHART is the default so that the number of trees at each score isoutput. If FD = HISTOGRAM, tree scores are pooled into classes, thesize of which is specified by the NCLASSES option.NCLASSES = integer-valueInteger-value specifies the number of class intervals for thefrequency distribution of tree scores. By default, NCLASSES=20, sothat adjacent tree scores are pooled into 20 classes of tree scores. Thisoption is only relevant when FD = HISTOGRAM.PAUP* 4.0 beta documentation February, 2002 35
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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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