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

Commands used in the PAUP BlockCommand ReferenceCUTOFFPCT = integer-valueUse CUTOFFPCT to specify the minimum bootstrap partitionfrequency to be displayed in the partition frequency table. Partitionsoccurring at a frequency below this value are not shown.ExampleIn the following example the BOOTSTRAP command is used to execute aheuristic search with random addition sequence on 200 bootstrap replicatedata sets. Optimal trees for each replicate are saved to a file named boot.tre.bootstrap nreps=200 treefile=boot.tresearch=heuristic/ addseq=random;CDUse the CD command to change the current working directory for theWindows, Unix and DOS versions.SyntaxCD ;Entering the command with no arguments simply reports the currentdirectory.CHARPARTITIONUse the CHARPARTITION to define a partition of the characters.SyntaxCHARPARTITION partition-name=partition-definition;The CHARPARTITION command is ordinarily issued from within the SETSblock described on page 22. However, you may also issue it from thecommand line or from within a PAUP block.CHARSETUse the CHARSET command to define a "character set." Character sets aresimply groups of characters that can be referred to by a single name in othercommands.SyntaxCHARSET character-set-name=character-list;42 February, 2002 PAUP* 4.0 beta documentation