Sample NEXUS Command Blocks

Table of Contents

• Sample NEXUS Sets Block
• Sample Command blocks for PAUP*
• Sample Command blocks for MrBayes

Sets block - edit values highlighted in RED to match your data.
begin sets;
  CHARSET COI=1-688;
  CHARSET 16S=689-1250;
  CHARSET morph=1251-1322;

  CHARSET COIpos1=1-688\3;
  CHARSET COIpos2=2-688\3;
  CHARSET COIpos3=3-688\3;
  
  TAXSET outgroup=taxon1 taxon2 taxon3;
  TAXSET NoMorph=taxon33 taxon38 taxon50;
  TAXSET COIonly=1-33;
  TAXSET beetles=22 25 27 33 35 40;
END;

 Simple Parsimony analysis - edit values highlighted in RED to match your data.
begin paup;

    log start replace=yes file=FILENAME_log.txt;

    set autoclose=yes criterion=parsimony root=outgroup storebrlens=yes increase=auto;

    outgroup MyOutgroup;

    hsearch addseq=random nreps=1000 swap=tbr hold=1;

    savetrees file=mytrees.tre format=altnex brlens=yes;

    contree all / majrule=yes strict=no treefile=myConsensustree.tre;
 
    log stop;

END;

 Parsimony Bootstrap analysis
begin paup;

    log start replace=yes file=FILENAME_log.txt;

    set autoclose=yes criterion=parsimony root=outgroup storebrlens=yes increase=auto;

    outgroup MyOutgroup;

    bootstrap nreps=1000 search=heuristic/ addseq=random nreps=10 swap=tbr hold=1;

    savetrees from=1 to=1 file=MyBootTree.tre format=altnex brlens=yes savebootp=NodeLabels MaxDecimals=0;

    log stop;
END;

Simple Maximum Likelihood analysis
begin paup;

    log start replace=yes file=FILENAME_log.txt;

    set criterion=distance autoclose=yes storebrlens=yes increase=auto root=outgroup;

    outgroup MyOutgroup;

    DSet distance=JC objective=ME base=equal rates=equal pinv=0 subst=all negbrlen=setzero;

    NJ showtree=no breakties=random;

    set criterion=like;

    Lset Base=(0.2892 0.2928 0.1309) Nst=6 Rmat=(3.7285 46.5293 1.3888 2.3793 16.4374)

    Rates=gamma Shape=0.9350 Pinvar=0.5691;

    hsearch addseq=random nreps=5 swap=tbr;

    savetrees file=MyML_tree.tre format=altnex brlens=yes maxdecimals=6;

    log stop;

 END;
    

Maximum Likelihood Bootstrap analysis
begin paup;

    log start replace=yes file=FILENAME_log.txt;
    
    set criterion=like autoclose=yes storebrlens=yes increase=auto root=outgroup;

    outgroup MyOutgroup;

    Lset Base=(0.2892 0.2928 0.1309) Nst=6 Rmat=(3.7285 46.5293 1.3888 2.3793 16.4374)

    Rates=gamma Shape=0.9350 Pinvar=0.5691;

    bootstrap nreps=1000 search=heuristic/ addseq=random swap=tbr hold=1;

    savetrees from=1 to=1 file=MyMLboot_tree.tre format=altnex brlens=yes savebootp=NodeLabels MaxDecimals=0;

    log stop;

END;
    

Partition Homogeneity test (a.k.a Incongruence Length Difference test)
Begin sets;
        charset Molecular = 1 - 650;
        charset Morphological = 651 - .;
    End;
    
begin paup;   
    set increase;
    log file=LetsLogResults.log append;
    charpartition P1 = Molecular:Molecular, Morphological:Morphological;

    exclude uninf ;
[because invariant and autapomorphic characters increase probability of false negatives in the ILD test]
    hompart partition=P1 nreps=1000 / start=stepwise addseq=random nreps=3  savereps=no randomize=addseq rstatus=no hold=1 swap=tbr multrees=yes timelimit=600;
  
[Do ILD test for datasets of partition P1, 1000 replicates, 3 random additions per replicate,
use TBR swapping, move on to next if random addition replicate takes longer than 10 minutes.]
      include all;
      log stop;
end;

MrBayes analysis using GTR+I+Γ - edit values highlighted in RED to match your data.
begin mrbayes;

    set autoclose=yes nowarn=yes;

    lset nst=6 rates=invgamma;

    mcmc ngen=10000000 relburnin=yes burninfrac=0.25 samplefreq=1000 printfreq=10000 nchains=4 savebrlens=yes;

    sump burnin=2500;

    sumt burnin=2500;

  END; 

Partitioned MrBayes analysis using mixed models
begin mrbayes;

    set autoclose=yes nowarn=yes;

    charset 1stpos = 1-720\3;

    charset 2ndpos = 2-720\3;

    charset 3rdpos = 3-720\3;

    partition bycodon = 3:1stpos,2ndpos,3rdpos;

    set partition = bycodon;

    unlink shape=(all) pinvar=(all) statefreq=(all) revmat=(all);

    prset applyto=(all) ratepr=variable;
 
    lset applyto=(1,3) nst=6 rates=invgamma;

    lset applyto=(2) nst=2 rates=gamma;

    mcmc ngen=10000000 relburnin=yes burninfrac=0.25 samplefreq=1000 printfreq=10000 nchains=4 savebrlens=yes;

    sump burnin=2500;

    sumt burnin=2500;

END;