Example MrBayes Command blocks [Simple DNA analysis with GTR+I+G:] begin mrbayes; Prset statefreqpr=dirichlet(1,1,1,1); lset nst=6 rates=invgamma; mcmc ngen=10000000 savebrlens=yes samplefreq=500 printfreq=500; end; [If the chains are not swapping add "mcmcp Temp=0.05;" before the mcmc command] [Example protein block (it will automatically select the best model)] begin mrbayes; lset rates=invgamma; prset aamodelpr=mixed; mcmc ngen=5000000 savebrlens=yes samplefreq=100 printfreq= 100; end; [Example complex block] begin mrbayes; charset SSU=1-950; charset LSU=951-1864; [this part defines the character sets] charset 5_8S=1865-2022; taxset no_ssu= Brasiliomyces_trina Erysiphe_galeopsidis Erysiphe_gracilis Microsphaera_pulchra Podosphaera_tridactyla [Missing SSU data for these taxa] Sarcoleotia_globosa Sawadaea_polyfida Uncinuliella_australiana Uncinuliella_simulans Clathrosporium_intricatum Spirosphaera_floriformis; outgroup Neolecta_irregularis; [set outgroup] delete no_ssu; [delete the taxa with missing SSU] partition rRNA = 3:SSU,LSU,5_8S; [setting the partitions] set partition=rRNA; lset applyto=(1) nst=6 rates=invgamma; lset applyto=(2) nst=6 rates=invgamma; lset applyto=(3) nst=6 rates=invgamma; prset applyto=(1) statefreqpr=dirichlet(1,1,1,1); [setting the models for each partition] prset applyto=(2) statefreqpr=dirichlet(1,1,1,1); prset applyto=(3) statefreqpr=fixed(equal); unlink pinvar=(all) shape=(all) revmat=(all) tratio=(all) statefreq=(all); [separating the partions in the analysis] mcmc temp=0.2 ngen=5000000 savebrlens=yes samplefreq=500 printfreq=500 startingtree=random; [running mcmc] end;