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

Commands used in the PAUP BlockCommand Referencerule consensus. A group must appear on more than thispercentage of the trees before it is retained. The default is 50.LE50 = YES|NOIf LE50 = YES is specified, groups occurring on less than 50%of the trees are retained in the consensus if they arecompatible with the groups already on the tree. LE50 = NOreverses the effect of a previous LE50 specification.GRPFREQ = YES|NOBy default, a table is output that shows all partitions (orgroups) occurring on at least one tree and the frequency ofeach such group. GRPFREQ = NO can be used to suppress thisoutput.ADAMS = YES|NOSpecify ADAMS = YES to request computation of an Adams consensustree. ADAMS = NO reverses the effect of a previous ADAMSspecification.USETREEWTS = YES|NOTrees output to a treefile in bootstrap and jackknife contain a weightcomment (see page 25). These weights are the reciprocal of thenumber of trees found in a replicate. The "GetTrees" commanddescribed on page 67 will optionally store these weights, and themajority-rule consensus calculator will use them when USETREEWTS= YES. This allows calculation of majority-rule consensus trees thatcorrespond exactly to the consensus tree output by the originalbootstrap or jackknife command. This option allows thecombination of bootstrap results from runs performed at differenttimes or on different machines and the recovery of results obtainedprior to a system crash. Also, it permits graphics-quality output ofbootstrap trees after redefining an outgroup or otherwise changingrooting options by rereading the trees (with weights) andcomputing/printing a majority-rule consensus tree.ExampleThe following example recalls bootstrap trees saved during three seperatebootstrap executions. See page 67 for information regarding the GETTREEScommand. By including the USETREEWTS option, the CONTREE commandwill display the bootstrap majority rule tree for the combined treescontained in the three seperate bootstap tree files.gettrees file=tfile1.out StoreTreeWts=yes mode=3;gettrees file=tfile2.out StoreTreeWts=yes mode=7;gettrees file=tfile3.out StoreTreeWts=yes mode=7;contree all/strict=no majrule=yes usetreewts=yes;INDICES = YES|NOSpecify INDICES to request calculation of a variety of consensus46 February, 2002 PAUP* 4.0 beta documentation