#NEXUS [----start Minimum evolution based tree searches----] set autoclose increase=auto; log file=MinEvolog1.txt replace; [!!!!!!!!MODELTEST HERE!!!!!!!!!!!!] Lset Base=(0.2705 0.2937 0.1381) Nst=6 Rmat=(1.6602 43.8290 0.6369 1.7869 10.4885) Rates=gamma Shape=1.3023 Pinvar=0.5660; outgroup 1; set criterion=distance; Dset distance=GTR [GTR/LogDet/TamNei//HKY85/F84/others...] rates=gamma [equal/gamma] shape=1.3023 [real-value] objective=ME [objective=ME objective=LSFit power=2;] Dcollapse=No [Yes/No] NegBrLen=SetZero; [Prohibit/Allow/SetZero] hsearch Start=nj [Stepwise/NJ/Current/Tree-number] AddSeq=Random [Simple/closest/AsIs/Random...] nreps=100 [integer-value] swap=TBR [TBR/SPR/NNI/None] NBest=No; [integer-value/No] DescribeTrees all/ Plot=Phylogram [None/Cladogram/Phylogram/Both] BrLens=Yes [Yes/No] LabelNode=Yes [Yes/No] Root=Outgroup [Outgroup/Lundberg/Midpoint] OutRoot=Monophyl; [Polytomy/Paraphy/Monophyl] savetrees brlens=No file=ME-GTR1.tre replace; savetrees brlens=Yes file=ME-GTR2.tre replace; [ClearTrees NoWarn=Yes; ]