PAUP* 4.0 GDE menus

Eric W. Linton elinton at rci.rutgers.edu
Wed Sep 25 19:29:58 EST 1996


Here are menus for using Paup* in GDE, remove this line and the signature
file at the end before pasteing. I hope everyone finds these useful.
# Copy and past into .GDEmenu file under the heading menu:Phylogeny

##################### READ ME PAUP* 4.0 Menus ########################
# Created by Eric W. Linton, Rutgers University during the Workshop  #
# on Molecular Evolution at Woods Hole Oceanographic Institute 1996. #
# This is given AS IS, I and especially Woods Hole have no liability.#
# Not every posible option availiable in PAUP is offered in these    #
# menus, some are not possible for an initial analysis, other were   #
# beyond the abilities of the GDE menuing system or myself. 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.Inappropriate choices cannot be greyed out in the GDE menus,#
# therefore choices that are used for only some of the analysis are  #
# labled for which type of analysis they can be used for. Choices    #
# that have defaults filled-in will not be placed into the PAUP      #
# command block unless they are used by the analysis type choosen.   #
#                                                                    # 
# GDE will create an "in" file called Pp.in for a Parsimony search,  #
# Pml.in for a Maximum Likelihood search or Pd.in for a Distance     #
# search. While PAUP is running you will be able to view the process,#
# if you are not running it in Batch mode, when the initial analysis #
# is finished you can view the output in the paup window and run     #
# additional analysis from the paup> or quit. All results are logged #
# to a file using PAUPs LOG command creating a second file Pp.in.log #
# for a Parsimony analysis Pml.in.log for Max. Like or Pd.in.log for #
# Distance. All saved trees will be in a file Pp.in.tre, Pml.in.tre  #
# or Pd.in.tre depending upon the analysis you ran. This file can be #
# opened with Treetool-there is a choice for this. All three files   #
# created by an analysis are left in you default directory. Unless   #
# you change their names they will be over-written the next time you #
# run the same type of
analysis.                                                                #
#                                                                    #
# 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 with THE MENUS not with PAUP, email me at    #
# elinton at rci.rutgers.edu and I will try to fix it, no guarantees.   #
######################################################################
item:PAUP* 4.0 Help
itemmethod:(echo 'help;' > help.paup; cmdtool paup help.paup; /bin/rm -f
help.paup;)&

item:Paup* 4.0 Parsimony
itemmethod: (readseq -a -f17 in1>Pp.in; /bin/rm -f gde*_*; echo 'Begin
PAUP;' >> Pp.in; echo 'LOG STart;' >> Pp.in; echo 'OUTGROUP $OGR/ONLY;' >>
Pp.in; echo 'SET CRITERION=parsimony;' >> Pp.in; echo 'SET OPt=$OTM;' >>
Pp.in; echo '$BEE $ADDS $KEP $SRT $SAP;' >> Pp.in; echo 'Contree
all/STrict=No $TOC=yes;' >> Pp.in; echo 'DESCRIBE $NTR/$TYP $ROT ;' >>
Pp.in; echo 'SAVETrees FILe=Pp.tre FMt=Phylip ROot=$RTO Brlens=$BLE
FRom=$FOM To=$TOO REplace=Yes;' >> Pp.in; echo 'end;' >> Pp.in; $TXT
$DISPLAY_FUNC)&

in:in1
informat:genbank
insave:
inmask:

arg:OGR
arglabel:Outgroup(s) Number(s)?
argtype:text

arg:OTM
arglabel:Optimization?
argtype:chooser
argchoice:Acctran:Acctran
argchoice:Deltran:Deltran
argchoice:MinF:Minf

arg:BEE
arglabel:Search Options:
argtype:choice_menu
argchoice:BandB Single Search:BandB 
argchoice:10 Bootstraps:BOOTSTRAP Bseed=12357 NReps=10 SEarch=Bandb/
argchoice:50 Bootstraps:BOOTSTRAP Bseed=12579 NReps=50 SEarch=Bandb/
argchoice:100 Bootstraps:BOOTSTRAP Bseed=12325 NReps=100 SEarch=Bandb/
argchoice:1000 Bootstraps:BOOTSTRAP Bseed=86357 NReps=1000 SEarch=Bandb/
argchoice:Heuristic Single Search:HSearch 
argchoice:10 Bootstraps:BOOTSTRAP Bseed=12353 NReps=10 SEarch=Heuristic/
argchoice:50 Bootstraps:BOOTSTRAP Bseed=12579 NReps=50 SEarch=Heuristic/
argchoice:100 Bootstraps:BOOTSTRAP Bseed=124657 NReps=100 SEarch=Heuristic/
argchoice:10 Faststep:BOOTSTRAP Bseed=1579 NReps=10 SEarch=Faststep
argchoice:100 Faststep:BOOTSTRAP Bseed=157873 NReps=100 SEarch=Faststep

arg:KEP
arglabel:Keep (minimal trees only type "No", for all trees = to or < type
"a real-value") (BandB and Heuristic Searches Only)
argtype:text

arg:ADDS
arglabel:Addition sequence? (BandB and Heuristic Only!)
argtype:choice_menu
argchoice:No:
argchoice:Furthest:ADdseq=Furthest Keep=
argchoice:As is:ADdseq=Asis Keep=
argchoice:Simple:ADdseq=Simple Keep=
argchoice:max-mini (BandB Only):ADdseq=Maxmini Keep=
argchoice:max-mini (k) (BandB Only):ADdseq=kmaxmini Keep=
argchoice:Random (Heuristic Only):ADdseq=Random Keep=
argchoice:Closest (Heuristic Only):ADdseq=Closest Keep=

arg:SRT
arglabel:Starting trees for branch swapping: (Heuristic Search Only)
argtype:chooser
argchoice:No:
argchoice:Stepwise:STARt=Stepwise NReps=$HRE RSEed=$REE
argchoice:Neighbor-Joining:STARt=NJ NReps=$HRE

arg:HRE
arglabel:Number of replicates: (Heuristic Search Only)
argtype:slider
argmin:1
argmax:10
argvalue:10

arg:REE
arglabel:Heuristic Odd seed number?
argtype:slider
argmin:1
argmax:1000
argvalue:671

arg:SAP
arglabel:Branch swapping algorithm: (Heuristic Search Only)
argtype:choice_menu
argchoice:No:
argchoice:No Swapping:SWap=NOne
argchoice:Nearest Neighbor Interchange:SWap=NNi
argchoice:SubTree Prunning Regrafting:SWap=Spr
argchoice:TreeBisection-Reconnection:SWap=Tbr

arg:TOC
arglabel:Consensus Tree Options:
argtype:chooser
argchoice:Strict:STrict
argchoice:Semi-Strict:SEmistrict
argchoice:Majority Rule:Majrule
argchoice:Adams:ADams

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

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

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

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

arg:FOM
arglabel:Save trees from Number:
argtype:slider
argmin:1
argmax:100
argvalue:1

arg:TOO
arglabel:Save trees to Number:
argtype:slider
argmin:1
argmax:1000
argvalue:100

arg:TXT
arglabel:Edit and Run Options:
argtype:chooser
argchoice:Just Run:cmdtool paup Pp.in;
argchoice:Edit and Run:textedit Pp.in; cmdtool paup Pp.in;
argchoice:Edit Only:textedit Pp.in;

arg:DISPLAY_FUNC
argtype:chooser
arglabel:View tree using treetool?
argchoice:Yes:treetool Pp.tre;
argchoice:No:

item:Paup* 4.0 Maximum Likelihood
itemmethod: (readseq -a -f17 in1>Pml.in; /bin/rm -f gde*_*; echo 'Begin
PAUP;' >> Pml.in; echo 'LOG STA;' >> Pml.in; echo 'OUTGROUP $OGR/ONLY;' >>
Pml.in; echo 'SET CRITERION=likelihood;' >> Pml.in; echo 'LSET $SUB $RATT
$BFQ  $VRT $SPV $STI $RON;' >> Pml.in; echo '$BEE $SRT $ADDS $SAP;' >>
Pml.in; echo 'Contree all/STrict=No $TOC;' >> Pml.in; echo 'DESCRIBE
$NTR/$TYP $ROT ;' >> Pml.in; echo 'SAVETrees FILe=Pml.tre FMt=Phylip $RTO
$BLE FRom=$FOM To=$TOO REplace=Yes;' >> Pml.in; echo 'end;' >> Pml.in;
$TXT $DISPLAY_FUNC)&

in:in1
informat:genbank
insave:
inmask:

arg:OGR
arglabel:Outgroup(s) Number(s)?
argtype:text

arg:SUB
arglabel:Base substitution model?
argtype:chooser
argchoice:Single:NSt=1
argchoice:Unequal:NSt=2 Tratio=

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

arg:BFQ
arglabel:Base fequency?
argtype:chooser
argchoice:Equal:Basefreq=EQual
argchoice:Empirical:Basefreq=Empirical

arg:VRT
arglabel:Two parameter model variant for Empirically derived base frequency?
argtype:choice_menu
argchoice:No:
argchoice:Haseqewa-Kishino-Yano (1985):Variant=HKY
argchoice:Felsenstein (1984):Variant=F84

arg:SPV
arglabel:Starting branch lengths?
argtype:chooser
argchoice:Rogers-Swofford method:Initbrlen=Rogers
argchoice:Fitch-Margoliash method:Initbrlen=FM

arg:STI
arglabel:Starting values for other parameters?
argtype:choice_menu
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:BEE
arglabel:Search Options:
argtype:choice_menu
argchoice:Heuristic Single Search:HSearch 
argchoice:10 Bootstraps:BOOTSTRAP Bseed=12357 NReps=10 SEarch=Heuristic/
argchoice:50 Bootstraps:BOOTSTRAP Bseed=12579 NReps=50 SEarch=Heuristic/
argchoice:10 Faststep:BOOTSTRAP Bseed=1579 NReps=10 SEarch=Faststep
argchoice:100 Faststep:BOOTSTRAP Bseed=157873 NReps=100 SEarch=Faststep

arg:SRT
arglabel:Starting trees for branch swapping: (Heuristic Searches Only)
argtype:choice_menu
argchoice:No:
argchoice:Stepwise:STARt=Stepwise
argchoice:Neighbor-Joining:STARt=NJ

arg:ADDS
arglabel:Addition sequence: (Heuristic Searches Only)
argtype:choice_menu
argchoice:No:
argchoice:Random:ADdseq=Random NReps=$HRE RSEed=$REE
argchoice:As is:ADdseq=Asis NReps=$HRE RSEed=$REE

arg:HRE
arglabel:Heuristic replicates:
argtype:slider
argmin:1
argmax:10
argvalue:10

arg:REE
arglabel:Heuristic Odd seed number?
argtype:slider
argmin:1
argmax:1000
argvalue:567

arg:SAP
arglabel:Branch swapping algorithm: (Heuristic Searches Only)
argtype:choice_menu
argchoice:No:
argchoice:No Swapping:SWap=NOne
argchoice:Nearest Neighbor Interchange:SWap=NNi
argchoice:SubTree Prunning Regrafting:SWap=Spr
argchoice:TreeBisection-Reconnection:SWap=Tbr

arg:TOC
arglabel:Consensus Tree Options:
argtype:chooser
argchoice:Strict:STrict=yes
argchoice:Semi-Strict:SEmistrict=yes
argchoice:Majority Rule:Majrule=yes
argchoice:Adams:ADams=yes

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

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

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:
argtype:slider
argmin:1
argmax:100
argvalue:1

arg:TOO
arglabel:Save trees to Number:
argtype:slider
argmin:1
argmax:1000
argvalue:100

arg:TXT
arglabel:Edit and Run Options:
argtype:chooser
argchoice:Just Run:cmdtool paup Pml.in;
argchoice:Edit and Run:textedit Pml.in; cmdtool paup Pml.in;
argchoice:Edit Only:textedit Pml.in;
 
arg:DISPLAY_FUNC
argtype:chooser
arglabel:View tree using treetool?
argchoice:Yes:treetool Pml.tre;
argchoice:No:

item:Paup* 4.0 Distance
itemmethod: (readseq -a -f17 in1>Pd.in; /bin/rm -f gde*_*; echo 'Begin
PAUP;' >> Pd.in; echo 'LOG STA;' >> Pd.in; echo 'OUTGROUP $OGR/ONLY;' >>
Pd.in; echo 'SET CRITERION=distance;' >> Pd.in; echo '$DTC $RTS $MID $SST
$NBL;' >> Pd.in; echo '$BEE $SRT $KEP $ADD $SAP;' >> Pd.in; echo 'Contree
all/STrict=No $TOC;' >> Pd.in; echo 'DESCRIBE $NTR / $TYP $ROT ;' >>
Pd.in; echo 'SAVETrees FILe=Pd.tre FMt=Phylip $RTO $BLE FRom=$FOM To=$TOO
REplace=Yes;' >> Pd.in; echo 'end;' >> Pd.in; $TXT $DISPLAY_FUNC)&

in:in1
informat:genbank
insave:
inmask:

arg:OGR
arglabel:Outgroup(s) Number(s)?
argtype:text

arg:DTC
arglabel:Choose distance method:
argtype:choice_menu
argchoice:Mean:DSET DIstance=MEan
argchoice:Absolute (# of differences):DSET DIstance=Abs
argchoice:Uncorrected ("P"):DSET DIstance=P
argchoice:Jukes-Cantor:DSET DIstance=Jc
argchoice:Felsenstein 81:DSET DIstance=F81
argchoice:Tajima-Nei:DSET DIstance=TAJnei
argchoice:Kimura 2-Parameter:DSET DIstance=K2p
argchoice:Felsenstein 84:DSET DIstance=F84
argchoice:Haseqewa-Kishino-Yano (1985):DSET DIstance=Hky85
argchoice:Kimura 3-Parameter:DSET DIstance=K3p
argchoice:Tamura-Nei:DSET DIstance=TAMnei
argchoice:General Time Reversible:DSET DIstance=Gtr
argchoice:LogDet/Paralinear:DSET DIstance=Logdet

arg:RTS
arglabel:Rates for variable sites?
argtype:chooser
argchoice:Equal:RAtes=Equal
argchoice:Gamma:RAtes=Gamma SHape=$SPE

arg:SPE
arglabel:Gamma Shape (Only applies if Gamma Choosen)
argtype:text
argtext:0.5

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

arg:SST
arglabel:Substitution restrictions-Estimate or count:
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:NBL
arglabel:Negative branch-length handling:
argtype:choice_menu
argchoice:Prohibit:Negbrlen=Prohibit
argchoice:Allow:Negbrlen=Allow
argchoice:Set to zero:Negbrlen=SETZero
argchoice:Set to absolute value:Negbrlen=SETAbsval

arg:BEE
arglabel:Search Options:
argtype:choice_menu
argchoice:Heuristic Single Search:HSearch
argchoice:10 Bootstraps:BOOTSTRAP Bseed=12357 NReps=10 SEarch=Heuristic/
argchoice:50 Bootstraps:BOOTSTRAP Bseed=12539 NReps=50 SEarch=Heuristic/
argchoice:10 Neighbor Joining:BOOTSTRAP Bseed=1239 NReps=10 SEarch=Nj
argchoice:100 Neighbor Joining:BOOTSTRAP Bseed=12397 NReps=100 SEarch=Nj
argchoice:10 Faststep:BOOTSTRAP Bseed=1579 NReps=10 SEarch=Faststep
argchoice:100 Faststep:BOOTSTRAP Bseed=157873 NReps=100 SEarch=Faststep

arg:SRT
arglabel:Starting trees for branch swapping: (Heuristic Searches Only)
argtype:chooser
argchoice:No:
argchoice:Stepwise:STARt=Stepwise Keep=
argchoice:Neighbor-Joining:STARt=NJ Keep=

arg:ADD
arglabel:Sequence additon: (Heuristic Searches Only)
argtype:chooser
argchoice:No:
argchoice:Random:ADdseq=Random NReps=$HRE RSEed=$REE
argchoice:As is:ADdseq=Asis NReps=$HRE RSEed=$REE

arg:KEP
arglabel:Keep (minimal trees only type "No", for all trees = to or < type
"a real-value") (Heuristic Searches Only)
argtype:text

arg:HRE
arglabel:Heuristic replicates:
argtype:slider
argmin:1
argmax:10
argvalue:10

arg:REE
arglabel:Heuristic Odd seed number?
argtype:slider
argmin:1
argmax:1000
argvalue:389

arg:SAP
arglabel:Branch swapping algorithm: (Heuristic Searches Only)
argtype:choice_menu
argchoice:No:
argchoice:No Swapping:SWap=NOne
argchoice:Nearest Neighbor Interchange:SWap=NNi
argchoice:SubTree Prunning Regrafting:SWap=Spr
argchoice:TreeBisection-Reconnection:SWap=Tbr

arg:TOC
arglabel:Consensus Tree Options:
argtype:chooser
argchoice:Strict:STrict=yes
argchoice:Semi-Strict:SEmistrict=yes
argchoice:Majority Rule:Majrule=yes
argchoice:Adams:ADams=yes

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

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

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:
argtype:slider
argmin:1
argmax:100
argvalue:1

arg:TOO
arglabel:Save trees to Number:
argtype:slider
argmin:1
argmax:1000
argvalue:100

arg:TXT
arglabel:Edit input before running?
argtype:chooser
argchoice:Just Run:cmdtool paup Pd.in;
argchoice:Edit and Run:textedit Pd.in; cmdtool paup Pd.in;
argchoice:Edit Only:textedit Pd.in;
 
arg:DISPLAY_FUNC
argtype:chooser
arglabel:View tree using treetool?
argchoice:Yes:treetool Pd.tre;
argchoice:No:

-- 
Eric Linton
Rutgers, The State University of New Jersey
Cell and Developmental Biology
E-mail: elinton at rci.rutgers.edu
web page: http://www.rci.rutgers.edu/~elinton
snail mail:
        Rutgers/Nelson Labs C-109
        P O Box 1059
        Piscataway, NJ 08855-1059




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