#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] [start writing to a log file; replace "your_log" with your log file name] log file=your_log.log; [execute your data file; replace "your_data" with your data file name execute your_data.nex;] [sets criterion to likelihood] set criterion=likelihood; [this is a model for HKHY+I+G; insert your best-fit model and estimated parameters instead] lset tratio=1.39027 basefreq=(0.24756 0.26029 0.27310) rates=gamma shape=0.630891 pinvar=0.160243; [defines constraint group where 1-11 are taxa to constrain to monophyly; replace "constrained_group_name" with your constraint group name: constraints constrained_group_name=((1-11))] constraints ibero=((C_macrole, C_occiden, C_arcasii, C_willkom, , C_duriens ,C_polylep,, C_lusitan, C_lemming, C_oretanu)); [does 10 heuristic search replicates enforcing constraints on taxa 1-11(above) with tbr branch swapping and random addition of taxa] hs enforce constraints=ibero addseq=rand swap=tbr nreps=10; [saves your constrained tree with branch lengths; replace "your_tree" with your tree file name you can then use this constrained tree, along with the unconstrained tree, for instance, in a file like «Shimodaira-Hasegawa.nex» to test whether the constrained tree is significantly different from the constrained tree] savetrees brlens file=your_tree.tree; [describes trees] describe; [stop writing to log file] log stop; end;