begin paup;
log   file=parsimony_search.log
      start;
execute parsimony.nxs;
set criterion=parsimony;
pset
	collapse=maxbrlen	[No|MaxBrlen|MinBrlen|AmbEqual]
	MSTaxa=uncertain 	[Uncertain|Polymorph|Variable]
	Opt=acctran		[AccTran|DelTran|MinF]
	StepMatrix=threeplus1	[ObsOnly|AllStates|ThreePlus1]
				[IncludeAnc=No|Yes,No]
				[AncStates=<ancstates-name>,<none>]
				[Goloboff=No|Yes,No]
				[GK=<integer-value>,2]
				[GUninf=Exclude|Include,Exclude]
				[GPeeWee=No|Yes,no]
				[MinForFit=MinLength|Range,MinLength]
				[GapMode=Missing|NewState,Missing]
	gapmode=missing;


BandB
	UpBound=0
	[Keep=<real-value>|No,No]
	[MulTrees=No|Yes,Yes]
	[Enforce=No|Yes,No]
	[Constraints=<constraint-name>,<none>]
	[Converse=No|Yes,No]
	[FDOnly=No|Yes,No]
	[FDType=BarChart|Histogram,BarChart]
	[FDClasses=<integer-value>,20]
	[FDFile=<frequency-distribution-file-name>,<none>]
	[Replace=No|Yes,*No]
	[AddSeq=Furthest|Asis|Simple|MaxMini|KMaxMini,Furthest]
	[Status=No|Yes,Yes]
	[DStatus=<integer-value>|None,60]
	DStatus=60;


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=parsimony.trees;
ClearTrees
      NoWarn=Yes;      
log stop;
end;
[================================================================]
[                       end tree search                          ]
[================================================================]
[================================================================]
[                         Bootstrapping:                         ]
[================================================================]
Begin paup;
log   file=parsboot.log
      start;
set criterion=parsimony;
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                            ]
[================================================================]