#NEXUS [starts PAUP] begin paup; set autoclose [closes the status window automatically] nowarntree [turns off the feature that prompts you to save trees in memory] nowarnreset [turns off feature that asks "do you really want to reset the data file"] torder=right [specifies the tree order to be ladderized to the right] flush [flushes the file buffer] tcompress=yes [prints trees in a compressed format, which allows you to view large trees in a single page] defaultmode [tells paup to use the default option when a dialog box is opened] increase=auto; set crit=p; log file=salaria_clade.mp.constraint.log append; outgroup Sfasciatu; constraint salarias (monophyly)= (Pruber,Psalensis,PASGAR,Sfasciatu,Cgalerita,Lpholis, ( pCR1, pGR2, pISR1, pISR2, pISR3, pISR4, pIT2, pIT3, pIT4, pIT5, pPT1, pPT2, pPT3, pSP1, pSP10, pSP11, pSP3, pSP4, pSP5, pSP6, pSP7, pSP8, pSP9, eGR1, eGR2, fCR2, fGR1, fGR2, fGR3,fGR4, fISR1, fISR2, fMRC1, fMRC2, fSP1, fSP10, fSP11, fSP12, fSP13, fSP2, fSP3, fSP4, fSP5, fSP6, fSP7, fSP8, fSP9, fTRK2, fTRK3 ) ) ; hsear enforce constraints=salarias addseq=rand swap=tbr nreps=10 timelimit=90; savetrees file=total.salaria_clade.mp.tre brlens; [ gettrees mode=7 file=total.unconstrain.mp.tre; pscores /nonparamtest=yes testdetails=yes khtest=yes scorefile=total.salarias.mp.contraint.txt; ] log stop; end;