#---------Made by Eric W. Linton 1996 rev. 1997, 1999 and 2003----------#

#                   INTALLATION INSTRUCTIONS
# 1) Make sure you have the most current version of PAUP*4.0 and name it "paup". For Mr. Bayes
#    make sure the program is named mb. For Modeltest it should be called modeltest.
#    The name must be in all lowercase with no * or number extensions. 
# 2) Place all the programs in the GDE/bin/ folder including the modelblock3.1 file.
# 3) Login as superuser so that you can modify the main .GDEmenus file. If you modify
#    this file then these programs will be available to all individual accounts on the Unix
#    machine. If you only want these menus available for a specific user then place a
#    copy of .GDEmeus in that users home directory, then changes made will ONLY be 
#    available to that user account.
# 4) Copy and past into .GDEmenus file BELOW the heading menu:Phylogeny
# 5) Make sure that the itemmethod: line for each item is ONE line with NO returns.
# 6) Save changes and open GDE, check the Phylogeny menu
# 6) GO TO PAUP* Instructions... FIRST.

#     ********** READ ME PAUP* 4.0 Menus Version 3 **********
# Created by Eric W. Linton, Michigan State Univesity during the Workshop  
# on Molecular Evolution at Woods Hole Marine Biological Lab Fall,   
# 1996. Last Revised January 2003.                                        
# This is given AS IS, I, Woods Hole and MSU have no liability.  
#
# All menus have been revised from the previous version including Help  
#                                                                    
# I have included many of the possible option availiable in the PAUP 
# Search menu from the Macintosh version. Since that is what I have  
# tried to duplicate here, I recommend getting the Mac version and   
# using it to learn the menus better. All options are preset to the  
# same defaults as they are in PAUP, so you can see what they are.   
# If there is a command not contained in the menus, this is where    
# you can use the edit feature to add other commands to the PAUP     
# command block. First learn the PAUP command line codes by          
# installing these menus and choosing PAUP* 4.0 Help, or read the    
# manual. You can save the "in" file created by these menus with or  
# without additional edits and run it in batch mode in the back-     
# ground.                                                            
#                     ***IMPORTANT***                                
# Inappropriate choices cannot be greyed out in the GDE menus.       
# These choices will not be placed into the PAUP command block,        
# unless they are used by the analysis type choosen.                 
# Choices are labled as to which ones go together.                   q                                        			                                 #                                                                    
# I have tried to make the interface as straight-forward as possible 
# Make sure you read the entire menu filling in ALL appropriate menu 
# choices. Any problems, comments or suggestions with THE MENUS not with    
# PAUP, email me at lintone@msu.edu and I will try to fix it, 
# no guarantees.   
#     ************************************************************

menu:PAUP* Menu
item:Make PAUP* Matrix File for Download
itemmethod:(readseq -a -f17 in1 > paup.nex; mkdir $MKD; mv -f paup.nex $MKD/$FLN.nex; /bin/rm -f gde*_*;)&

in:in1
informat:genbank
insave:
inmask:

arg:MKD
arglabel:Project Directory (NO SPACES USE _ or -)
argtype:text

arg:FLN
arglabel:Filename:(.nex automatically added)
argtype:text


item:Make MrBayes Matrix File for Download
itemmethod:(readseq -a -f17 in1 > mrb.in;  echo 'Begin mrbayes;' >> mrb.in; echo \ >> mrb.in; echo 'end ;' >> mrb.in; sed "s/interleave/interleave=yes/" <mrb.in> mrb.in2; rm -f mrb.in; mkdir $MKD; mv -f mrb.in2 $MKD/$FLN_MrB.nex; )&
itemhelp:mrb.help

in:in1
informat:genbank
insave:
inmask:

arg:MKD
arglabel:Project Directory (NO SPACES USE _ or -)
argtype:text

arg:FLN
arglabel:Filename:(_MrB.nex automatically added)
argtype:text

item:________________________
itemmethod:

item:Modeltest3.06
itemmethod:(readseq -a -f17 in1 > .modeltest.in;  cat .modeltest.in /usr/local/biotools/GDE/bin/modelblock3.1 > .modeltest2.in; mkdir $MKD; mv -f .modeltest2.in $MKD/$FLN_MT.nex; /bin/rm -f gde*_*; cd $MKD/; xterm -e paup $FLN_MT.nex; modeltest < model.scores > $FLN_MT.results; mv model.scores $FLN_MT.scores; mv modelfit.log $FLN_MT.log; textedit $FLN_MT.results; )&
itemhelp:modeltest.help

in:in1
informat:genbank
insave:
inmask:

arg:MKD
arglabel:Project Directory (NO SPACES USE _ or -)
argtype:text

arg:FLN
arglabel:Filename:(_MT.nex automatically added)
argtype:text

arg:INFORMATION
arglabel:INSTRUCTIONS
argtype:choice_list
argchoice:Fill-in the Project Directory and Filename
argchoice:Have the taxa and mask you want to analyse chosen then click OK.
argchoice:Paup will run, then modeltest, then the results will appear.
argchoice:Now use the results to set-up Max Like using the normal Paup menus.
argchoice:REMEMBER unless the model is JC, K2P, F81, F84 or HKY USE the GTR model.

item:________________________
itemmethod:
item:PAUP* 4 Instructions
itemmethod:

arg:INFORMATION
arglabel:INSTRUCTIONS
argtype:choice_list
argchoice:1) Choose a Criterion: Parsimony, Maximum Likelihood, or Distance
argchoice:2) Set Criterion Options for Parsimony, Maximum Likelihood, or Distance
argchoice:3) Choose a Search: Heuristic, Bandb, Exhaustive; or Cluster Method: NJ/UPGMA-Distance ONLY
argchoice:3a) Choose Evaluate Random Trees... (Optional)
argchoice:4) Choose Tree Options...
argchoice:5) Choose Run Options...

item:Help...
itemmethod:(echo '#NEXUS' > help.paup; echo 'SET PAUSE=MSG;' >> help.paup; echo $HCU >> help.paup; echo 'end;' >> help.paup; xterm -e paup help.paup; /bin/rm -f help.paup;)&

in:in1
informat:genbank
insave:
inmask:

arg:HCU
arglabel:Choose the level of help you want:
argtype:chooser
argchoice:Usage Summary:'$HLP ?;' >> help.paup;
argchoice:Detailed Information:'Help $HLP;' >> help.paup;

arg:HLP
arglabel:Help on:
argtype:choice_menu
argchoice:Defaults:Defaults
argchoice:DSet:DSet         
argchoice:Edit:Edit           
argchoice:Execute:Execute       
argchoice:Factory:Factory        
argchoice:FStatus:FStatus 
argchoice:Help:Help  
argchoice:Leave:Leave 
argchoice:Log:Log          
argchoice:Quit:Quit     
argchoice:Set:Set        
argchoice:ToNEXUS:ToNEXUS 
argchoice:*Agree:Agree
argchoice: AllTrees:AllTrees
argchoice: AncStates:AncStates
argchoice: Assume:Assume
argchoice: BandB:BandB
argchoice: BaseFreqs:BaseFreqs
argchoice: Bootstrap:Bootstrap
argchoice: CharPartition:CharPartition
argchoice: CharSet:CharSet
argchoice:*ClearTrees:ClearTrees
argchoice: Condense:Condense
argchoice:*Constraints:Constraints
argchoice:*ConTree:ConTree
argchoice: CStatus:CStatus
argchoice: CType:CType
argchoice:*Delete:Delete
argchoice:*Deroot:Deroot
argchoice:*Describe:Describe
argchoice: DinucFreqs:DinucFreqs
argchoice: DScores:DScores
argchoice: Exclude:Exclude
argchoice: ExSet:ExSet
argchoice: Filter:Filter
argchoice: GammaPlot:GammaPlot 
argchoice:*GetTrees:GetTrees
argchoice: HomPart:HomPart
argchoice: HSearch:HSearch
argchoice: Include:Include
argchoice:*Ingroup:Ingroup
argchoice: Jackknife:Jackknife
argchoice: Lake:Lake
argchoice:*LoadConstr:LoadConstr
argchoice: LScores:LScores
argchoice: LSet:LSet
argchoice: MPRSets:MPRSets
argchoice: NJ:NJ
argchoice:*Outgroup:Outgroup
argchoice: Permute:Permute
argchoice: PScores:PScores
argchoice: PSet:PSet
argchoice: RandTrees:RandTrees
argchoice:*RateSet:RateSet
argchoice: Reconstruct:Reconstruct
argchoice:*Restore:Restore
argchoice: RevFilter:RevFilter
argchoice: Reweight:Reweight
argchoice:*Root:Root
argchoice: SaveAssum:SaveAssum
argchoice: SaveDist:SaveDist
argchoice:*SaveTrees:SaveTrees
argchoice: ShowAnc:ShowAnc
argchoice:*ShowConstr:ShowConstr
argchoice: ShowDist:ShowDist
argchoice: ShowMatrix:ShowMatrix
argchoice: ShowParts:ShowParts
argchoice: ShowRateSets:ShowRateSets
argchoice:*ShowTrees:ShowTrees
argchoice: ShowUserTypes:ShowUserTypes 
argchoice: SurfCheck:SurfCheck
argchoice:*TaxSet:TaxSet
argchoice:*TreeDist:TreeDist
argchoice:*TreeInfo:TreeInfo
argchoice:*TStatus:TStatus
argchoice: TypeSet:TypeSet
argchoice:*Undelete:Undelete
argchoice: UPGMA:UPGMA
argchoice: UserType:UserType
argchoice: Weights:Weights
argchoice: Wts:Wts
argchoice: WtSet:WtSet

item:Set Criterion...
itemmethod:(readseq -a -f17 in1 > PAUP.in; /bin/rm -f gde*_*; echo 'Begin PAUP;' >> PAUP.in; echo 'LOG STart;' >> PAUP.in; echo ' $OTR;' >> PAUP.in; echo 'SET CRITERION=$PIN TOrder=Left Taxlabels=Full;' >> PAUP.in;)&

in:in1
informat:genbank
insave:
inmask:

arg:PIN
arglabel:Analysis: (MUST CHOOSE)
argtype:chooser
argchoice:Parsimony:p
argchoice:Maximum Likelihood:l
argchoice:Distance:d

arg:OTR
arglabel:Outgroup root?
argtype:chooser
argchoice:Yes:OUTGROUP $OGR/ONLY
argchoice:No:

arg:OGR
arglabel:Outgroup(s) Number(s): (e.g. 1 4 11 20-25)
argtype:text

item:________________________
itemmethod:

item:Parsimony Options...
itemmethod:(echo 'PSET $GBF $COL $ANC $OTM $STM $MTS $GPM;' >> PAUP.in;)&

arg:GBF
arglabel:Use Goloboff fit criterion? (General Search Option)
argtype:chooser
argchoice:No:Goloboff=No
argchoice:Yes:Goloboff=Yes GK=$GKN

arg:GKN
arglabel:Goloboff K=<integer value>
argtype:text
argtext:0

arg:COL
arglabel:Collapse branch lengths... (General Search Option)
argtype:choice_menu
argchoice:if maximum length zero:Collapse=MaxBrlen
argchoice:if minimum length zero ("amb-"):Collapse=MinBrlen
argchoice:if MPR-sets are identical ("amb="):Collapse=AmbEqual
argchoice:No:Collapse=No

arg:ANC
arglabel:Include Ancestor in searches? (General Search Option)
argtype:chooser
argchoice:No:IncludeAnc=No
argchoice:Yes:IncludeAnc=Yes AncStates=$ANS

arg:ANS
arglabel:Ancestor States Name?
argtype:text

arg:OTM
arglabel:Character States Optimization: (Ordered (Wagner) and Unordered (Fitch))
argtype:chooser
argchoice:Acctran:OPt=AccTran
argchoice:Deltran:OPt=Deltran
argchoice:MinF:OPt=Minf

arg:STM
arglabel:Stepmatrix Options: (For Internal Node Assignments)
argtype:chooser
argchoice:All States:StepMatrix=AllStates
argchoice:Observed Only:StepMatrix=ObsOnly
argchoice:3+1 Rule:StepMatrix=ThreePlus1
argvalue:2

arg:MTS
arglabel:Multistate Taxa:Interpret multiple states as
argtype:chooser
argchoice:Uncertain:MSTaxa=Uncertain
argchoice:Polymorphism:MSTaxa=Polymorph
argchoice:Variable:MSTaxa=Variable

arg:GPM
arglabel:Treat Gaps as
argtype:chooser
argchoice:Missing:GapMode=Missing
argchoice:New State (5th base or 21st AA):GapMode=NewState
argvalue:1

arg:XXX
arglabel:PUSH (OK) THEN CHOOSE A Search Option AND/OR Evaluate Random Trees!
argtype:text

item:Maximum Likelihood Options...
itemmethod:(echo 'LSET $SUB $BFQ PInvar=$POIS $RTS $SPV $STI $RON;' >> PAUP.in;)&

arg:SUB
arglabel:Base substitution model:
argtype:chooser
argchoice:Unequal Ti/Tv ratio ("2 ST"):NSt=2 Tratio=$RATT
argchoice:Equal ("1 St"):NSt=1 
argchoice:General time-reversible ("6 ST"):NSt=6 Rmatrix=$RTX

arg:RATT
arglabel:Ti/Tv ratio for Unequal base substitution rate: (Real-Value or Estimate)
argtype:text
argtext:2

arg:RTX
arglabel:GTR ("6 ST") Rate matrix: ((<rAC><rAG><rAT><rCG><rCT>) or Estimate)
argtype:text
argtext:(1.0 1.0 1.0 1.0 1.0)

arg:BFQ
arglabel:Base fequency:
argtype:chooser
argchoice:Empirical:Basefreq=Empirical $VRT 
argchoice:Equal:Basefreq=EQual
argchoice:Set to:Basefreq=$STT $VRT

arg:STT
arglabel:Set to:(<frqA><frqC><frqG>)
argtype:text
argtext:(0.25 0.25 0.25)

arg:VRT
arglabel:Two parameter model variant: (Unequal Base Sub. with Empirical or Set to Base Freq.)
argtype:choice_menu
argchoice:Haseqewa-Kishino-Yano (1985):Variant=HKY
argchoice:Felsenstein (1984):Variant=F84

arg:POIS
arglabel:Proportion of Invariable sites: (<real-value> or Estimate)
argtype:text
argtext:0

arg:RTS
arglabel:Amoung-site rate variation:
argtype:chooser
argchoice:Equal:RAtes=Equal
argchoice:Gamma distribution:RAtes=Gamma SHape=$SPE NCat=$NCT $RCR

arg:SPE
arglabel:Gamma shape parameter: (Gamma distribution)
argtype:text
argtext:0.5

arg:NCT
arglabel:Number of categories: (Gamma distribution)
argtype:text
argtext:4

arg:RCR
arglabel:Represent category rates by: (Gamma distribution)
argtype:chooser
argchoice:Mean:RepRate=Mean
argchoice:Median:RepRate=Median

arg:SPV
arglabel:Starting branch lengths:
argtype:chooser
argchoice:Rogers-Swofford method:Initbrlen=Rogers
argchoice:Fitch-Margoliash method:Initbrlen=FM
argchoice:Use arbitrary length <real number>:Initbrlen=$ARB

arg:ARB
arglabel:Arbitrary length:
argtype:text
argtext:0.1

arg:STI
arglabel:Starting values for other parameters:
argtype:chooser
argchoice:Parsimony based approximations:STartvals=ParsApprox
argchoice:Arbitrary values:STartvals=Arbitrary

arg:RON
arglabel:Method for estimating ancestrial state reconstruction:
argtype:chooser
argchoice:Marginal:RECon=Marginal
argchoice:Joint:RECon=Joint

arg:XXX
arglabel:PUSH (OK) THEN CHOOSE A Search Option OR Neighbor Joining (FOR ML as a D option) AND/OR Evaluate Random Trees!
argtype:text

item:Distance Options...
itemmethod:(echo 'DSET $DTC $OJF $NBL;' >> PAUP.in;)&

arg:DTC
arglabel:Choose distance method:
argtype:choice_menu
argchoice:1 Total character differences:DIstance=Total
argchoice:2 Mean character differences:DIstance=MEan
argchoice:3 Absolute (# of differences):DIstance=Abs $MID $SST
argchoice:4 Uncorrected ("P"):DIstance=P PInvar=$PPV $RPB $MID $SST
argchoice:5 Jukes-Cantor:DIstance=Jc PInvar=$PPV $RPB $RTS $MID $SST
argchoice:6 Felsenstein 81:DIstance=F81 PInvar=$PPV $RPB $RTS $MID $SST
argchoice:7 Tajima-Nei:DIstance=TAJnei PInvar=$PPV $RPB $RTS $MID SUbst=All
argchoice:8 Kimura 2-Parameter:DIstance=K2p PInvar=$PPV $RPB $RTS $MID $SST
argchoice:9 Felsenstein 84:DIstance=F84 PInvar=$PPV $RPB $RTS $MID $SST
argchoice:10 Haseqewa-Kishino-Yano (1985):DIstance=Hky85 PInvar=$PPV $RPB $RTS $MID $SST
argchoice:11 Kimura 3-Parameter:DIstance=K3p PInvar=$PPV $RPB $RTS $MID $SST
argchoice:12 Tamura-Nei:DIstance=TAMnei PInvar=$PPV $RPB $RTS $MID $SST
argchoice:13 General Time Reversible:DIstance=Gtr PInvar=$PPV $RPB $RTS $MID $SST
argchoice:14 LogDet/Paralinear:DIstance=Logdet PInvar=$PPV $RPB $MID $SST
argchoice:15 Maximum Likelihood (Go Set ML Options...):DIstance=ML SUbst=All

arg:PPV
arglabel:Proportion of sites presumed to be Invariable (0 to 1) (For 4-14) 
argtype:text
argtext:0

arg:RPB
arglabel:Remove Proportions for each base: (When Invariable NOT equal to 0)
argtype:choice_menu
argchoice:Invariable=0:
argchoice:Proportional to base frequency:RemoveFreq=proportional $EFS $ASAS
argchoice:Equal proportiona for each base:RemoveFreq=equal $ASAS

arg:EFS
arglabel:Base frequency estimated from: (For Proportional Only)
argtype:chooser
argchoice:All sites:EstFreq=All
argchoice:Constant sites only:EstFreq=Constant

arg:ASAS
arglabel:Adjust for mean number of subs. over all sites: (When Invariable NOT equal to 0)
argtype:chooser
argchoice:No:AllSitesMean=No
argchoice:Yes:AllSitesMean=Yes

arg:RTS
arglabel:Rates for variable sites: (For 5-13)
argtype:chooser
argchoice:Equal:RAtes=Equal
argchoice:Gamma:RAtes=Gamma SHape=$SPE

arg:SPE
arglabel:Gamma Shape:
argtype:text
argtext:0.5

arg:MID
arglabel:Treatment of "missing-data" sites (and gaps) and ambiguity codes: (For 3-14)
argtype:chooser
argchoice:Infer:MIssdist=Infer
argchoice:Ignor:MIssdist=IGnor

arg:SST
arglabel:Substitution restrictions-Estimate or count: (For 3-15) (7 & 15 All subs. ONLY)
argtype:choice_menu
argchoice:All substitutions:SUbst=All
argchoice:Transversions only:SUbst=TV
argchoice:Transitions only:SUbst=TI
argchoice:Ti/Tv ratio:SUbst=TRatio

arg:OJF
arglabel:Objective functions: (1-15)
argtype:choice_menu
argchoice:Minimum Evolution:Objective=ME
argchoice:Unweighted least squares fit (Power=0):Objective=LSFit Power=0
argchoice:Weighted least squares Inverse weighting (Power=1):Objective=LSFit Power=1
argchoice:Weighted least squares Inverse-squared weighting (Power=2):Objective=LSFit Power=2

arg:NBL
arglabel:Negative branch-length handling: (1-15)
argtype:chooser
argchoice:Set to zero:Negbrlen=SetZero
argchoice:Prohibit:Negbrlen=Prohibit
argchoice:Allow:Negbrlen=Allow
argchoice:Set to absolute value:Negbrlen=SETAbsval

arg:XXX
arglabel:PUSH (OK) THEN CHOOSE A Search Option OR Neighbor Joining AND/OR Evaluate Random Trees!
argtype:text

item:________________________
itemmethod:

item:FastStep (Bootstrap Only) Options...
itemmethod:(echo 'BOOTSTRAP Bseed=$RSD NReps=$NRP ConLevel=$CTF SEarch=FastStep;' >> PAUP.in;)&

arg:NRP
arglabel:Number of Bootstrap Repetitions: (N)
argtype:text
argtext:1000

arg:RSD
arglabel:Repetition Seed Number:
argtype:text
argtext:1

arg:CTF
arglabel:Consensus tree frequency > N%
argtype:text
argtext:50

item:Heuristic Options...
itemmethod:(echo '$BEE $SRT Keep=$KEP $SAP ;' >> PAUP.in;)&

arg:BEE
arglabel:Search type:
argtype:chooser
argchoice:Single Search:HSearch 
argchoice:N Bootstraps:BOOTSTRAP Bseed=$RSD NReps=$NRP ConLevel=$CTF SEarch=Heuristic/ 

arg:NRP
arglabel:Number of Bootstrap Repetitions: (N)
argtype:text
argtext:1000

arg:RSD
arglabel:Repetition Seed Number: (Bootstrap Analysis Only)
argtype:text
argtext:1

arg:CTF
arglabel:Consensus tree frequency > N% (Bootstrap Analysis Only)
argtype:text
argtext:50

arg:KEP
arglabel:Keep minimal trees only "0" OR for all trees = or < "a real-value" ("0" Bootstrap)
argtype:text
argtext:0

arg:SRT
arglabel:Starting trees for branch swapping:
argtype:chooser
argchoice:Stepwise:STARt=Stepwise $ADDS
argchoice:Neighbor-Joining (ML & D Only):STARt=NJ

arg:ADDS
arglabel:Stepwise Addition Options:
argtype:chooser
argchoice:As is:ADdseq=Asis
argchoice:Random:ADdseq=Random NReps=$HRE RSEed=$RSD
argchoice:Simple (P Only):ADdseq=Simple
argchoice:Closest (P Only):ADdseq=Closest
argvalue:1

arg:HRE
arglabel:Number of Replicates: (Random Addition Only)
argtype:text
argtext:100

arg:RSD
arglabel:Replicate Seed Number: (Random Addition Only)
argtype:text
argtext:1

arg:SAP
arglabel:Branch swapping algorithm:
argtype:choice_menu
argchoice:No Swapping:SWap=NOne
argchoice:Nearest Neighbor Interchange:SWap=NNi
argchoice:SubTree Prunning Regrafting:SWap=Spr
argchoice:TreeBisection-Reconnection:SWap=TBR
argvalue:3

arg:XXX
arglabel:PUSH (OK) THEN CHOOSE Evaluate Random Trees... OR Tree Options...
argtype:text

item:BandB Options...
itemmethod:(echo '$BEE $ADDS Upbound=$UBD Keep=$KEP ;' >> PAUP.in;)&

arg:BEE
arglabel:Search type:
argtype:chooser
argchoice:Single Search:BandB 
argchoice:N Bootstraps:BOOTSTRAP Bseed=$RSD NReps=$NRP ConLevel=$CTF SEarch=Bandb/ 

arg:NRP
arglabel:Number of Bootstrap Repetitions: (N)
argtype:text
argtext:1000

arg:RSD
arglabel:Repetition Seed Number: (Bootstrap Analysis Only)
argtype:text
argtext:1

arg:CTF
arglabel:Consensus tree frequency > N% (Bootstrap Analysis Only)
argtype:text
argtext:50

arg:UBD
arglabel:Initial Upper bounds-Compute via stepwise "0" OR Set to "a real-value" ("0" Bootstrap)
argtype:text
argtext:0

arg:KEP
arglabel:Keep minimal trees only "0" OR for all trees = or < "a real-value" ("0" Bootstrap)
argtype:text
argtext:0

arg:ADDS
arglabel:Stepwise Addition Options:
argtype:chooser
argchoice:As is:ADdseq=Asis
argchoice:Furthest (P Only):ADdseq=Furthest 
argchoice:Simple (P Only):ADdseq=Simple
argchoice:max-mini (P Only):ADdseq=maxmini
argchoice:max-mini(k) (P Only):ADdseq=kmaxmini

arg:XXX
arglabel:PUSH (OK) THEN CHOOSE Evaluate Random Trees... OR Tree Options...
argtype:text

item:Exhaustive Options...
itemmethod:(echo 'Alltrees FD=$EFD $FFD Keep=$KEP $STSF ;' >> PAUP.in;)&

arg:EFD
arglabel:Tree-score frequencey distribution:
argtype:choice_menu
argchoice:Histogram with "N" classes:Histogram NClasses=$ECL
argchoice:Simple bar-chart (P Only):BarChart
argchoice:No:

arg:ECL
arglabel:Number of Histogram classes "N"?
argtype:text
argtext:20

arg:FFD
arglabel:Save frequency distribution of tree scores to file <name>?
argtype:chooser
argchoice:No:
argchoice:Yes:FDFile=$FDN Replace=Yes

arg:FDN
arglabel:Frequency distribution of tree scores file name:
argtype:text

arg:KEP
arglabel:Keep minimal trees only "0" OR for all trees = or < "a real-value"
argtype:text
argtext:0

arg:STSF
arglabel:Save tree scores to file <name>?
argtype:chooser
argchoice:No:
argchoice:Yes:ScoreFile=$STF Replace=Yes

arg:STF
arglabel:Tree score file name:
argtype:text

arg:XXX
arglabel:PUSH (OK) THEN CHOOSE Evaluate Random Trees... OR Tree Options...
argtype:text

item:Evaluate Random Trees...
itemmethod: (echo 'RandTrees NReps=$ERT TSeed=$TSD FDtype=$EFD $FFD ;' >> PAUP.in;)&

arg:ERT
arglabel:Number of Random Trees to Generate:
argtype:text
argtext:1000

arg:TSD
arglabel:Random Seed Number:
argtype:text
argtext:1

arg:EFD
arglabel:Tree-score frequencey distribution:
argtype:choice_menu
argchoice:Histogram with "N" classes:Histogram NClasses=$ECL
argchoice:Simple bar-chart (P Only):BarChart

arg:ECL
arglabel:Number of Histogram classes "N"?
argtype:text
argtext:20

arg:FFD
arglabel:Save frequency distribution of random trees to file <name>?
argtype:chooser
argchoice:No:
argchoice:Yes:FDFile=$FDN Replace=Yes

arg:FDN
arglabel:Frequency distribution of random trees file name:
argtype:text

arg:XXX
arglabel:NOW PUSH (OK) BUTTON THEN CHOOSE Tree Options...
argtype:text

item:________________________
itemmethod:

item:Neighbor Joining/UPGMA (Distance Only)...
itemmethod:(echo '$BEE ;'>> PAUP.in;)&

arg:PIN
arglabel:Set Distance Options First
argtype:chooser
argchoice:!:

arg:BEE
arglabel:Cluster type:
argtype:chooser
argchoice:Single Cluster:$AGM $MTD $BRS $BKT
argchoice:N Bootstraps:$AGM $MTD ShowTree=No; BOOTSTRAP Bseed=$RSD NReps=$NRP SEarch=$AGM

arg:AGM
arglabel:Algorithm
argtype:chooser
argchoice:NJ:NJ
argchoice:UPGMA:UPGMA

arg:MTD
arglabel:Use BioNJ Method
argtype:chooser
argchoice:No:BioNJ=No
argchoice:Yes:BioNJ=Yes

arg:NRP
arglabel:Number of Bootstrap Repetitions: (N)
argtype:text
argtext:1000

arg:RSD
arglabel:Repetition Seed Number: (Bootstrap Analysis Only)
argtype:text
argtext:1

arg:BRS
arglabel:Show Branch Lengths? (Single Cluster Only)
argtype:choice_menu
argchoice:No:BrLens=No
argchoice:Yes:BrLens=Yes

arg:BKT
arglabel:Break ties: (Single Cluster Only)
argtype:choice_menu
argchoice:Systematically (taxon-order dependent):BreakTies=Systematic
argchoice:Randomly, initial seed number = N:BreakTies=Random TieSeed=$RBK

arg:RBK
arglabel:Seed Number "N" (Single Cluster)
argtype:text
argtext:1

arg:XXX
arglabel:PUSH (OK) THEN CHOOSE Tree Options...
argtype:text

item:________________________
itemmethod:

item:Tree Options...
itemmethod: (echo 'Contree all/ Strict=No GrpFreq=No $TOC ;' >> PAUP.in ; echo 'DESCRIBE $NTR / LabelNode=No $TYP $ROT ;' >> PAUP.in ; echo 'SAVETrees FMt=Nexus $RTO $BLE FRom=$FOM To=$TOO REplace=Yes;' >> PAUP.in ; echo 'end;' >> PAUP.in  ;)&

arg:TOC
arglabel:Consensus Tree Options:
argtype:chooser
argchoice:Strict:STrict=Yes
argchoice:Semi-Strict:SEmistrict=yes
argchoice:Adams:ADams=yes 
argchoice:Majority Rule:MajRule=yes Percent=$CFF
argvalue:3

arg:CFF
arglabel:Majority Rule Cutoff N%:
argtype:text
argtext:50

arg:NTR
arglabel:Describe trees Number(s) or All:
argtype:text
argtext:All

arg:ROT
arglabel:Rooting:
argtype:chooser
argchoice:Outgroup:Root=Outgroup $OTT
argchoice:Lundberg:Root=Lundberg
argchoice:Midpoint:Root=Midpoint

arg:OTT
arglabel:Outgroup rooting:
argtype:chooser
argchoice:Polytomy:OUtroot=Polytomy
argchoice:Paraphyletic:OUtroot=PAraphy
argchoice:Monophyletic:OUtroot=Monophy
argvalue:2

arg:TYP
arglabel:Plot Type?
argtype:chooser
argchoice:Cladogram:PLot=Cladogram
argchoice:Phylogram:PLot=Phylogram
argchoice:Both:PLot=Both
argchoice:None:PLot=None

arg:RTO
arglabel:Root saved trees?
argtype:chooser
argchoice:No:ROot=No
argchoice:Yes:ROot=Yes

arg:BLE
arglabel:Save branch lengths?
argtype:chooser
argchoice:No:Brlens=No
argchoice:Yes:Brlens=Yes

arg:FOM
arglabel:Save trees from Number:(0=All)
argtype:text
argtext:0

arg:TOO
arglabel:Save trees to Number:(0=All)
argtype:text
argtext:0

arg:XXX
arglabel:NOW PUSH (OK) BUTTON THEN CHOOSE Run Options...
argtype:text

item:Run Options...
itemmethod:(mkdir $MKD; mv -f PAUP.in $MKD/$PIN.nex;  $TXT )&

arg:TXT
arglabel:Edit input before running?
argtype:chooser
argchoice:Just Run:xterm -e paup $MKD/$PIN.nex ;
argchoice:Edit and Run:textedit $MKD/$PIN.nex ; xterm -e paup $MKD/$PIN.nex ;
argchoice:Edit Only:textedit $MKD/$PIN.nex ;

arg:MKD
arglabel:Project Directory (NO SPACES USE _ or -)
argtype:text

arg:PIN
arglabel:File Name (NO SPACES USE _ OR -) .nex automatically added
argtype:text

item:========================
itemmethod:

#-------End-------#