begin paup;
log   file=ml.log
      start;
execute ml.nxs;
set criterion=likelihood;
lset
      nst=6                   [1/2/6]
      basefreq=empirical      [empirical/estimate/equal/fA fC fG]
      rates=Gamma             [equal/Gamma]
      ncat=4                 [integer-value]
      shape=estimate          [integer-value/estimate]
      PInvar=estimate         [PInvar=real-value/estimate/previous]
      RMatrix=estimate;       [RMatrix=rAC rAG rAT rCG rCT/Estimate/1 1 1 1 1]
                              [Variant= HKY/F84]
                              [TRatio=estimate/realvalue/previous]                             
                              [Recom=marginal/joint]                                           
                              [AllProbs=Yes/no]
                              [tserBrLens=Yes/No]
                              [Clock=Yes/No]
hsearch
      Start=Stepwise          [Stepwise/NJ/Current/Tree-number]
      AddSeq=Random           [Simple/closest/AsIs/Random...]
      nreps=10[1]             [integer-value]
      swap=TBR                [TBR/SPR/NNI/None]
      NBest=No;               [integer-value/No]
                              [Enforce=No/Yes]
                              [Constraints=Treefile name]
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=Yes
      file=GTR_Gamma.trees;
ClearTrees
      NoWarn=Yes;      
log stop;
end;
[================================================================]
[                       end tree search                          ]
[================================================================]
[================================================================]
[                         Bootstrapping:                         ]
[================================================================]
Begin paup;
log   file=MLboot.log
      start;
set criterion=likelihood;
lset
      nst=6
      basefreq=empirical     
      rates=gamma
      ncat=8
      shape=previous
      PInvar=previous
      RMatrix=previous;
BootStrap
      nreps=100         [integer-value]
      ConLevel=50       [integer-value]
      GrpFreq=Yes       [yes/no]
      CutOffPct=5       [integer value]
      search=heuristic [Heuristic/BandB/FastStep]
      / nreps=1;
Log stop;
end;

[================================================================]
[                       end bootstrap                            ]
[================================================================]

ompare the trees found with Neighbor Joining and Minimum Evolution