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

Commands used in the PAUP BlockCommand Referencetaxon_1 0taxon_2 1 0taxon_3 2 3 0taxon_4 4 5 6taxon_5 7 8 9taxon_6 11 12 13taxon_4 0taxon_5 10 0taxon_6 14 15 0;As in the CHARACTERS block, new line characters in interleavedmatrices are significant, in that they indicate a switch to a new taxon.TAXLABELSTAXLABELS allows one to specify the names and ordering of the taxa. Thiscommand serves to define taxa, and is allowed only if the NEWTAXA tokenis included in the DIMENSIONS statement.MATRIXThe MATRIX command contains the distance data.Commands used in the PAUP BlockCommands described in this section are specific to PAUP*. They may beincluded in the PAUP block of a NEXUS file or typed from the commandline.Unless otherwise specified, options specified in these commands are"persistent;" i.e., they retain their values between successful invocations ofthe command. Persistence of options simplifies typing of commandsbecause one a command requiring a large number of options has beenentered once, subsequent invocations of the command need not respecifyall of the options. The drawback is that you can become temporarilyconfused if you forget that a previously specified option remains in effectuntil you explicitly override it.OPTIONS AND SUBCOMMANDS AFFECTING MULTIPLE COMMANDSSeveral options apply to a number of commands. Specification of theseoptions on one command affects all commands that use the same options.To minimize redundancy, these options are described in the followingsections rather than in the description for each individual command towhich the option applies.30 February, 2002 PAUP* 4.0 beta documentation