# 	WARNING:	this file is created automatically
 # 	edit		ARB_GDEmenus.source and MENUS/xxx.menu instead
 # 	and run make in this directory

 # 	To get more information read GDE2.2_manual_text
 #	I added two new argtypes:
 #		argtype:tree	A list of trees in the database
 #		argtype:weights A list of conservation profiles in the db



lmenu:export
item:Export Sequences only to Foreign Format (using readseq: slow) ...
 
itemmethod:arb_readseq in1 -pipe -all -form=$FORMAT > $OUTPUTFILE
itemhelp:readseq.help

arg:FORMAT
argtype:choice_menu
argchoice:GenBank:genbank
argchoice:IG/Stanford:ig
argchoice:NBRF:nbrf
argchoice:EMBL:embl
argchoice:GCG:gcg
argchoice:DNA Strider:strider
argchoice:Fitch:fitch
argchoice:Pearson/Fasta:pearson
argchoice:Zuker:zuker
argchoice:Olsen:olsen
argchoice:Phylip:phylip
argchoice:Plain text:raw
argchoice:ASN.1:asn
argchoice:PIR:pir
argchoice:MSF:msf
argchoice:PAUP:paup
argchoice:Pretty:pretty -nametop -nameleft=3 -numright -nameright -numtop

arg:OUTPUTFILE
argtype:text
arglabel:Save as?

in:in1
informat:genbank


lmenu:pretty_print
item:Pretty Print Sequences (slow) ...
 





itemmethod:arb_readseq in1 -p -a -f=pretty $NAMELEFT $NAMERIGHT $NUMTOP $NUMBOT $NUMLEFT $NUMRIGHT -col=$COLS -width=$WIDTH $MATCH $GAPC > in1.pretty; (arb_textprint in1.pretty; /bin/rm -f in1 in1.pretty )&
itemhelp:readseq.help
in:in1
informat:genbank
 
arg:NAMETOP
argtype:chooser
arglabel:Names at top  ?
argchoice:No:
argchoice:Yes:-nametop
 
arg:NAMELEFT
argtype:chooser
arglabel:Names at left ?
argchoice:No:
argchoice:Yes:-nameleft
 
arg:NAMERIGHT
argtype:chooser
arglabel:Names at right?
argchoice:Yes:-nameright
argchoice:No:
 
arg:NUMTOP
argtype:chooser
arglabel:Numbers at top  ?
argchoice:Yes:-numtop
argchoice:No:
 
arg:NUMBOT
argtype:chooser
arglabel:Numbers at tail ?
argchoice:No:
argchoice:Yes:-numbot
 
arg:NUMLEFT
argtype:chooser
arglabel:Numbers at left ?
argchoice:Yes:-numleft
argchoice:No:
 
arg:NUMRIGHT
argtype:chooser
arglabel:Numbers at right?
argchoice:Yes:-numright
argchoice:No:

arg:MATCH
argtype:chooser
arglabel:Show difference to current species?
argchoice:No:
argchoice:Yes:-match
 
arg:GAPC
argtype:chooser
arglabel:Count gap symbols?
argchoice:No:
argchoice:Yes:-gap
 
arg:WIDTH
argtype:slider
arglabel:Sequence width?
argmin:10
argmax:200
argvalue:100
 
arg:COLS
argtype:slider
arglabel:Column spacers?
argmin:0
argmax:50
argvalue:10
 


lmenu:import
item:Import Sequences in Foreign Format (using readseq: slow !!) ...
 



itemmethod:arb_readseq $INPUTFILE -a -f2 > OUTPUTFILE
itemhelp:readseq.help

arg:INPUTFILE
argtype:text
arglabel:Name of foreign file?

out:OUTPUTFILE
outformat:genbank

 

item:Test arb_jim ...


itemmethod:arb_jim
itemhelp:jim.help


out:OUTPUTFILE
outformat:genbank

 


menu:align
arb_item:Clustalv Alignment (DNA)
itemmethod:(tr '"%//' '>' <in1 >clus_in; ${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ; /bin/rm -f clus_in* in1)

itemhelp:clustal_help

arg:KTUP
argtype:slider
arglabel:K-tuple size for fast pairwise search 
argmin:1
argmax:10
argvalue:2

arg:WIN
argtype:slider
arglabel:Window size
argmin:1
argmax:10
argvalue:4

arg:Trans
argtype:chooser
arglabel:Transitions weighted?
argchoice:Yes:/TRANSIT
argchoice:No:

arg:FIXED
argtype:slider
arglabel:Fixed gap penalty
argmin:1
argmax:100
argvalue:10

arg:FLOAT
arglabel:Floating gap penalty
argtype:slider
argmin:1
argmax:100
argvalue:10

in:in1
informat:flat
insave:

out:out1
outformat:flat


item:Clustalw DNA Alignment
itemmethod:(tr '"%//' '>' <in1 >clus_in;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ; /bin/rm -f clus_in* in1)

itemhelp:clustal.help

arg:KTUP
argtype:slider
arglabel:K-tuple size for fast pairwise search
argmin:1
argmax:10
argvalue:2

arg:WIN
argtype:slider
arglabel:Window size for fast pairwise search
argmin:1
argmax:10
argvalue:4

arg:MATRIX_
argtype:chooser
arglabel:Weighting matrix
argchoice:BLOSUM:BLOSUM
argchoice:PAM:PAM
argchoice:GONNET:GONNET
argchoice:ID:ID

arg:FIXED_
argtype:slider
arglabel:Gap Open Panelty
argmin:1
argmax:100
argvalue:8.7
 
arg:FLOAT_
arglabel:Gap Extend Panelty
argtype:slider
argmin:.001
argmax:1
argvalue:.1


in:in1
informat:flat
insave:

out:out1
outformat:flat


item:Clustalw Protein Alignment
itemmethod:(tr '"%//' '>' <in1 >clus_in;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ;\/bin/rm -f clus_in* in1)


itemhelp:clustalw.help

arg:KTUP_
argtype:slider
arglabel:K-tuple size for fast pairwise search
argmin:1
argmax:10
argvalue:2

arg:WIN_
argtype:slider
arglabel:Window size and top diagonals for fast alignment
argmin:1
argmax:10
argvalue:4

arg:MATRIX_
argtype:chooser
arglabel:Weighting matrix
argchoice:BLOSUM:BLOSUM
argchoice:PAM:PAM
argchoice:GONNET:GONNET
argchoice:ID:ID

arg:FIXED_
argtype:slider
arglabel:Gap Open Panelty
argmin:1
argmax:100
argvalue:8.7
 
arg:FLOAT_
arglabel:Gap Extend Panelty
argtype:slider
argmin:.001
argmax:1
argvalue:.1


 
in:in1
informat:flat
insave:

out:out1
outformat:flat

item:Assemble Contigs
itemmethod: (tr '"%//' '>' <in1 >in1.tmp;CAP2 in1.tmp $OVERLAP $PMATCH >  out1;/bin/rm -f in1.tmp)
itemhelp:CAP2.help

arg:OVERLAP
argtype:slider
arglabel:Minimum overlap?
argmin:5
argmax:100
argvalue:20

arg:PMATCH
argtype:slider
arglabel:Percent match required within overlap
argmin:25
argmax:100
argvalue:90

in:in1
informat:flat

out:out1
outformat:gde



menu:user
item: Start a slave arb on a foreign host ...

itemmethod: ${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait"  &

arg:dis
argtype:text
arglabel:hostname of slave host ?


 


menu:DNA/RNA
item:Translate...
itemmethod:Translate -tbl $TBL -frame $FRAME -min_frame $MNFRM $LTRCODE $NOSEP in1 > out1

arg:FRAME
argtype:chooser
arglabel:Which reading frame?
argchoice:First:1
argchoice:Second:2
argchoice:Third:3
argchoice:All six:6

arg:MNFRM
arglabel:Minimum length of NT sequence to translate?
argtype:slider
argmin:0
argmax:500
argvalue:20
 
arg:LTRCODE
argtype:chooser
arglabel:Translate to:
argchoice:Single letter codes:
argchoice:Triple letter codes:-3

arg:NOSEP
argtype:chooser
arglabel: Seperate?
argchoice:No:
argchoice:Yes:-sep
 
arg:TBL
arglabel:Codon table?
argtype:chooser
argchoice:mycoplasma:2
argchoice:universal:1
argchoice:yeast:3
argchoice:Vert. mito.:4

in:in1
informat:gde
 
out:out1
outformat:gde
 
item:Dot plot
itemmethod:(DotPlotTool in1 ; /bin/rm -f in1)&
itemhelp:DotPlotTool.help

in:in1
informat:gde
insave:


item:Clustal alignment
itemmethod:(tr '"%//' '>' <in1 >clus_in;cp in1 test; ${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ; /bin/rm -f clus_in* in1)

itemhelp:clustal_help

arg:KTUP
argtype:slider
arglabel:K-tuple size for pairwise search
argmin:1
argmax:10
argvalue:2

arg:WIN
argtype:slider
arglabel:Window size
argmin:1
argmax:10
argvalue:4

arg:Trans
argtype:chooser
arglabel:Transitions weighted?
argchoice:Yes:/TRANSIT
argchoice:No:

arg:FIXED
argtype:slider
arglabel:Fixed gap penalty
argmin:1
argmax:100
argvalue:10

arg:FLOAT
arglabel:Floating gap penalty
argtype:slider
argmin:1
argmax:100
argvalue:10


in:in1
informat:flat
insave:

out:out1
outformat:flat



item:Variable Positions
itemmethod:varpos $REV < in1 > out1

arg:REV
argtype:chooser
arglabel:Highlight (darken)
argchoice:Conserved positions:
argchoice:variable positions:-rev

in:in1
informat:flat

out:out1
outformat:colormask




item:MFOLD
itemmethod:(tr 'a-z' 'A-Z' < seqGB > .GDE.tmp.caps; ZUKERGDE.sh .GDE.tmp.caps $CT $ARBHOME/GDEHELP/ZUKER/ > out1 && $METHOD < out1; Zuk_to_gen < $CT >file.gen; gde file.gen& ${ARB_TEXTEDIT:-textedit} RegionTable )&
itemhelp:MFOLD.help

in:seqGB
informat:genbank
insave:

arg:METHOD
argtype:chooser
arglabel:RNA type
argchoice:Fold Linear RNA:lrna
argchoice:Fold Circular RNA:crna

arg:CT
argtype:text
arglabel:Pairing(ct)  File Name
argtext:mfold_out


item:Draw Secondary structure
itemmethod:(LoopTool $TEMPLATE in1 ; /bin/rm -f in1) &
itemhelp:LoopTool.help

arg:TEMPLATE
argtype:chooser
arglabel:Use template file ./loop.temp?
argchoice:No:
argchoice:Yes:-t loop.temp

in:in1
informat:genbank
insave:


item:blastn
itemmethod:(sed "s/[//%]/>/" <in1 > in1.f; blastn $BLASTDB in1.f W=$WORDLEN M=$MATCH N=$MMSCORE > in1.tmp; ${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1*)&
itemhelp:blast.help

in:in1
informat:flat
insave:

arg:BLASTDB
argtype:choice_menu
arglabel:Which Database
argchoice:genbank:$ARBHOME/GDEHELP/BLAST/genbank
argchoice:genbank update:$ARBHOME/GDEHELP/BLAST/genupdate

arg:WORDLEN
argtype:slider
arglabel:Word Size
argmin:4
argmax:18
argvalue:12

arg:MATCH
argtype:slider
arglabel:Match Score
argmin:1
argmax:10
argvalue:5

arg:MMSCORE
argtype:slider
arglabel:Mismatch Score
argmin:-10
argmax:-1
argvalue:-5

item:blastx
itemmethod:(sed "s/[//%]/>/" <in1 > in1.f; cp $ARBHOME/GDEHELP/BLAST/PAM??? .; blastx $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE> in1.tmp; ${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1* PAM???)&
itemhelp:blast.help

in:in1
informat:flat
insave:

arg:BLASTDB
argtype:choice_menu
arglabel:Which Database
argchoice:pir1:$ARBHOME/GDEHELP/BLAST/pir
argchoice:genpept:$ARBHOME/GDEHELP/BLAST/genpept

arg:WORDLEN
argtype:slider
arglabel:Word Size
argmin:1
argmax:5
argvalue:3

arg:Matrix
arglabel:Substitution Matrix:
argtype:choice_menu
argchoice:PAM120:PAM120
argchoice:PAM250:PAM250

arg:CODE
argtype:choice_menu
arglabel:Genetic Code
argchoice:Standard or Universal:0
argchoice:Vertebrate Mitochondrial:1
argchoice:Yeast Mitochondrial:2
argchoice:Mold Mitochondrial and Mycoplasma:3
argchoice:Invertebrate Mitochondrial:4
argchoice:Ciliate Macronuclear:5
argchoice:Protozoan Mitochondrial:6
argchoice:Plant Mitochondrial:7
argchoice:Echinodermate Mitochondrial:8


item:FASTA (DNA/RNA)
itemmethod:(sed "s/[//%]/>/"<in1 >in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; ${ARB_TEXTEDIT:-textedit} in1.out;\rm in1*) &
itemhelp:FASTA.help

in:in1
informat:flat

arg:DBASE
argtype:choice_menu
arglabel:Database
argchoice:GenBank Primate:$ARBHOME/GDEHELP/FASTA/GENBANK/gbpri.seq\ 1
argchoice:GenBank Rodent:$ARBHOME/GDEHELP/FASTA/GENBANK/gbrod.seq\ 1
argchoice:GenBank all Mammal:$ARBHOME/GDEHELP/FASTA/GENBANK/gbmam.seq\ 1
argchoice:GenBank verteBrates:$ARBHOME/GDEHELP/FASTA/GENBANK/gbvrt.seq\ 1
argchoice:GenBank Inverts:$ARBHOME/GDEHELP/FASTA/GENBANK/gbinv.seq\ 1
argchoice:GenBank pLants:$ARBHOME/GDEHELP/FASTA/GENBANK/gbpln.seq\ 1
argchoice:GenBank Struct RNA:$ARBHOME/GDEHELP/FASTA/GENBANK/gbrna.seq\ 1
argchoice:GenBank euk. Organelles:$ARBHOME/GDEHELP/FASTA/GENBANK/gborg.seq\ 1
argchoice:GenBank phaGe:$ARBHOME/GDEHELP/FASTA/GENBANK/gbphg.seq\ 1
argchoice:GenBank bacTeria:$ARBHOME/GDEHELP/FASTA/GENBANK/gbbct.seq\ 1
argchoice:GenBank sYnthetic:$ARBHOME/GDEHELP/FASTA/GENBANK/gbsyn.seq\ 1
argchoice:GenBank Viral:$ARBHOME/GDEHELP/FASTA/GENBANK/gbvrl.seq\ 1
argchoice:GenBank Unannotated:$ARBHOME/GDEHELP/FASTA/GENBANK/gbuna.seq\ 1

arg:NUMOFALN
argtype:slider
arglabel:Number of Alignment to Report
argmin:1
argmax:100
argvalue:20

arg:MATRIX
arglabel:Which SMATRIX
argtype:choice_menu
argchoice:Default:
argchoice:altdiag.mat:-s $ARBHOME/GDEHELP/FASTA/MATRIX/altdiag.mat
argchoice:altprot.mat:-s $ARBHOME/GDEHELP/FASTA/MATRIX/altprot.mat
argchoice:dna.mat:-s $ARBHOME/GDEHELP/FASTA/MATRIX/dna.mat
argchoice:prot.mat:-s $ARBHOME/GDEHELP/FASTA/MATRIX/prot.mat


menu:Protein
item:Clustal Protein Alignment
itemmethod:(tr '"%//' '>' <in1 >clus_in;cp in1 test; ${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ; /bin/rm -f clus_in* in1)


itemhelp:clustal_help

arg:KTUP
argtype:slider
arglabel:K-tuple size for pairwise search
argmin:1
argmax:10
argvalue:2

arg:WIN
argtype:slider
arglabel:Window size
argmin:1
argmax:10
argvalue:4

arg:Matrx
argtype:chooser
arglabel:Weighting matrix
argchoice:PAM 250:PAM250
argchoice:PAM 100:PAM100
argchoice:Identity:ID

arg:FIXED
argtype:slider
arglabel:Fixed gap penalty
argmin:1
argmax:100
argvalue:10
 
arg:FLOAT
arglabel:Floating gap penalty
argtype:slider
argmin:1
argmax:100
argvalue:10


 
in:in1
informat:flat
insave:

out:out1
outformat:flat

item:blastp
itemmethod:(sed "s/[//%]/>/" <in1 > in1.f; cp $ARBHOME/GDEHELP/BLAST/PAM??? .; blastp $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1* PAM???)&
itemhelp:blast.help

in:in1
informat:flat
insave:

arg:BLASTDB
argtype:choice_menu
arglabel:Which Database
argchoice:pir:$ARBHOME/GDEHELP/BLAST/pir
argchoice:genpept:$ARBHOME/GDEHELP/BLAST/genpept
argchoice:local:$ARBHOME/GDEHELP/BLAST/local_db

arg:Matrix
arglabel:Substitution Matrix:
argtype:choice_menu
argchoice:PAM120:PAM120
argchoice:PAM250:PAM250

arg:WORDLEN
argtype:slider
arglabel:Word Size
argmin:1
argmax:5
argvalue:3

item:tblastn
itemmethod:(sed "s/[//%]/>/" <in1 > in1.f; cp $ARBHOME/GDEHELP/BLAST/PAM??? .; tblastn $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE > in1.tmp; ${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1* PAM???)&
itemhelp:blast.help

in:in1
informat:flat
insave:

arg:BLASTDB
argtype:choice_menu
arglabel:Which Database
argchoice:genbank:$ARBHOME/GDEHELP/BLAST/genbank
argchoice:genbank update:$ARBHOME/GDEHELP/BLAST/genupdate

arg:Matrix
arglabel:Substitution Matrix:
argtype:choice_menu
argchoice:PAM120:PAM120
argchoice:PAM250:PAM250

arg:WORDLEN
argtype:slider
arglabel:Word Size
argmin:4
argmax:18
argvalue:12

arg:CODE
argtype:choice_menu
arglabel:Genetic Code
argchoice:Standard or Universal:0
argchoice:Vertebrate Mitochondrial:1
argchoice:Yeast Mitochondrial:2
argchoice:Mold Mitochondrial and Mycoplasma:3
argchoice:Invertebrate Mitochondrial:4
argchoice:Ciliate Macronuclear:5
argchoice:Protozoan Mitochondrial:6
argchoice:Plant Mitochondrial:7
argchoice:Echinodermate Mitochondrial:8

item:blast3
itemmethod:(sed "s/[//%]/>/" <in1 > in1.f; cp $ARBHOME/GDEHELP/BLAST/PAM??? .; blast3 $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1* PAM???)&
itemhelp:blast3.help

in:in1
informat:flat
insave:

arg:BLASTDB
argtype:choice_menu
arglabel:Which Database
argchoice:pir1:$ARBHOME/GDEHELP/BLAST/pir
argchoice:genpept:$ARBHOME/GDEHELP/BLAST/genpept

arg:Matrix
arglabel:Substitution Matrix:
argtype:choice_menu
argchoice:PAM120:PAM120
argchoice:PAM250:PAM250

arg:WORDLEN
argtype:slider
arglabel:Word Size
argmin:1
argmax:5
argvalue:3

item:FASTA (Protein)
itemmethod:(sed "s/[//%]/>/"<in1 >in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; ${ARB_TEXTEDIT:-textedit} in1.out;\rm in1*) &
itemhelp:FASTA.help

in:in1
informat:flat

arg:DBASE
argtype:choice_menu
arglabel:Database
argchoice:NBRF PIR1:$ARBHOME/GDEHELP/FASTA/PIR/pir1.dat\ 2
argchoice:NBRF PIR2:$ARBHOME/GDEHELP/FASTA/PIR/pir2.dat\ 2
argchoice:NBRF PIR3:$ARBHOME/GDEHELP/FASTA/PIR/pir3.dat\ 2


arg:NUMOFALN
argtype:slider
arglabel:Number of Alignment to Report
argmin:1
argmax:100
argvalue:20

arg:MATRIX
arglabel:Which SMATRIX
argtype:choice_menu
argchoice:Default:
argchoice:Minimum mutation matrix:-s $ARBHOME/GDEHELP/FASTA/MATRIX/codaa.mat
argchoice:Identity matrix:-s $ARBHOME/GDEHELP/FASTA/MATRIX/idnaa.mat
argchoice:Identity matrix for mismatches:-s $ARBHOME/GDEHELP/FASTA/MATRIX/idpaa.mat
argchoice:PAM250:-s $ARBHOME/GDEHELP/FASTA/MATRIX/pam250.mat
argchoice:PAM120:-s $ARBHOME/GDEHELP/FASTA/MATRIX/pam120.mat



menu:Seq management
item:Assemble Contigs
itemmethod:(sed "s////>/"<in1 >in1.tmp; CAP2 in1.tmp $OVERLAP $PMATCH > out1;/bin/rm -f in1.tmp)
itemhelp:CAP2.help

arg:OVERLAP
argtype:slider
arglabel:Minimum overlap?
argmin:5
argmax:100
argvalue:20

arg:PMATCH
argtype:slider
arglabel:Percent match required within overlap
argmin:25
argmax:100
argvalue:90

in:in1
informat:flat

out:out1
outformat:gde
outoverwrite:

item:Map View
itemmethod:(mapview in1 -pbl $PBL -npp $NPP; /bin/rm -f in1)&
itemhelp:mapview.help

in:in1
informat:gde
insave:

arg:PBL
arglabel:Pixel Between Lines
argtype:slider
argvalue:10
argmin:1
argmax:15

arg:NPP
arglabel:Nucleotides Per Pixel
argtype:slider
argvalue:1
argmin:1
argmax:20

arg:LWIDTH
arglabel:Line Thickness
argtype:slider
argvalue:2
argmin:1
argmax:5


item:Restriction sites
itemmethod:(cp $ENZ in1.tmp ; $PRE_EDIT Restriction in1.tmp in1 > out1 ; rm in1.tmp; cp out1 tmp );
itemhelp:Restriction.help

arg:ENZ
argtype:text
arglabel:Enzyme file
argtext:$ARBHOME/GDEHELP/DATA_FILES/enzymes

arg:PRE_EDIT
argtype:chooser
arglabel:Edit enzyme file first?
argchoice:Yes:${ARB_TEXTEDIT:-textedit} in1.tmp;
argchoice:No: 

in:in1
informat:flat

out:out1
outformat:colormask





















menu:SAI
item:Positional Variability by Olsons dnamlrates (max 5000 Species, 8000 seqlength) 
itemmethod:(/bin/rm -f outfile infile treefile ;(echo C F M T U L;echo C 35; echo M 10; echo T 2.0 ) |arb_convert_aln -GenBank in1 -phylip2 in1.ph;echo 1 >>in1.ph; arb_export_tree $TREE >>in1.ph;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ;echo done )&
itemhelp:phylip.help

arg:TREE
argtype:tree
arglabel:Base Tree
argchoice:tree_main

in:in1
informat:genbank
inmask:
insave:


menu:Incremental_Phylogeny
item:FastDnaMl (max 500 Species) ...
itemmethod:(/bin/rm -f outfile infile treefile ;(echo Y F Q G T R "`arb_export_rates $RATES`";echo G 0 0; echo T 2.0 ) |arb_convert_aln -GenBank in1 -phylip2 infile;arb_export_tree $TREE >>infile;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ; rm in1 )&
itemhelp:phylip.help

arg:RATES
argtype:weights
arglabel:Select a Weighting Mask
argchoice:POS_VAR_BY_PARS

arg:TREE
argtype:tree
arglabel:Base Tree
argchoice:tree_main

arg:DISPLAY_FUNC
argtype:chooser
arglabel:What to do with the tree:?
argchoice:ARB ('tree_fml_//'):arb_read_tree tree_fml_$$ treefile "PRG=FASTDNAML FILTER=$FILTER PKG=olsen/felsenstein RATE=$RATES"
argchoice:Treetool:treetool treefile


in:in1
informat:genbank
inmask:
insave:


menu:Phylogeny
item:DeSoete Tree fit
itemmethod: ( ${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ;/bin/rm -f in1* )&
itemhelp:lsadt.help

in:in1
informat:genbank
insave:
inmask:

arg:CORR
arglabel:Dist. correction?
argtype:chooser
argchoice:Olsen:-c=olsen
argchoice:Jukes/Cantor:-c=jukes
argchoice:None:-c=none

arg:INIT
arglabel:Parameter estimate
argtype:choice_menu
argchoice:uniformly distributed random numbers:1
argchoice:error-perturbed data:2
argchoice:original distance data from input matrix:3

arg:SEED
argtype:slider
arglabel:Random nr. seed
argmin:0
argmax:65535
argvalue:12345
 
arg:DISPLAY_FUNC
argtype:chooser
arglabel:View tree using
argchoice:ARB ('tree_desoete'):arb_read_tree tree_desoete_$$ in1.out "PRG=DeSoete CORR=$CORR FILTER=$FILTER"
argchoice:TextEdit:${ARB_TEXTEDIT:-textedit} in1.out 
argchoice:Treetool:treetool in1.out

item:Phylip Distance Methods ( Original Phylip, Interactiv )
itemmethod:(	/bin/rm -f treefile infile outfile; arb_convert_aln -GenBank  in1  -phylip infile ;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ;	/bin/rm -f  in1  infile outfile treefile 	)&
 
arg:DISPLAY_FUNC
argtype:chooser
arglabel:What to do with the tree:?
argchoice:ARB ('tree_ph_xxx'):(arb_read_tree tree_ph_$$ treefile "FILTER=$FILTER PKG=phylip")
argchoice:TextEdit:${ARB_TEXTEDIT:-textedit} outfile
argchoice:Treetool:treetool treefile

arg:PROGRAM
arglabel:Which method?
argtype:chooser
argchoice:DNADIST:mv -f infile outfile
argchoice:Fitch:${ARB_XCMD:-cmdtool} fitch
argchoice:Kitsch:${ARB_XCMD:-cmdtool} kitsch
argchoice:Neighbor:${ARB_XCMD:-cmdtool} neighbor

arg:DPGM
arglabel:Treat data as..
argtype:chooser
argchoice:DNA:dnadist
argchoice:RNA:dnadist
argchoice:AA:protdist


in:in1
informat:genbank
inmask:sdfgdfg
insave:


 
 

item:Phylip Distance Methods ( Simple GUI Based Interface )
itemmethod:(	/bin/rm -f treefile infile outfile; arb_convert_aln -GenBank  in1  -phylip infile ;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ;	/bin/rm -f  in1  infile outfile treefile 	)&
itemhelp:phylip.help
 
arg:DISPLAY_FUNC
argtype:chooser
arglabel:What to do with the tree:?
argchoice:ARB ('tree_ph_xxx'):($CORRECTION;echo||$DPGM;arb_read_tree tree_ph_$$ treefile "PRG=$PROGRAM CORR=$TEXT FILTER=$FILTER PKG=phylip")
argchoice:TextEdit:${ARB_TEXTEDIT:-textedit} outfile
argchoice:Treetool:treetool treefile

arg:PROGRAM
arglabel:Which method?
argtype:chooser
argchoice:Neighbor:neighbor
argchoice:Fitch:fitch
argchoice:Kitsch:kitsch

arg:DPGM
arglabel:Treat data as..
argtype:chooser
argchoice:DNA/RNA:(arb_echo $DNAFLAGS |dnadist);TEXT=$DNATEXT
argchoice:AA:(arb_echo $PROFLAGS |protdist);TEXT=$PROTEXT

arg:CORRECTION
arglabel:Correction DNA/PROT
argtype:chooser
argchoice:Kimura  / Dayhoff:		DNATEXT=kimura;		DNAFLAGS="y";		PROTEXT=dayhoff;	PROFLAGS="y"
argchoice:Jin_Nei / Kimura:		DNATTEXT=jinnai;	DNAFLAGS="d y";		PROTEXT=kimura;		PROFLAGS="p y"
argchoice:Max.Lik./(George/Hunt/Barker):DNATEXT=maxlik;		DNAFLAGS="d d y";	PROTEXT=ghb;		PROFLAGS="p p y"
argchoice:JukesC. / Chemical:		DNATEXT=jc;		DNAFLAGS="d d d y";	PROTEXT=chemical;	PROFLAGS="p p a c y"
argchoice:JukesC. / Hall:		DNATEXT=jc;		DNAFLAGS="d d d y";	PROTEXT=hall;		PROFLAGS="p p a h y"
argchoice:USER    / USER:		DNATEXT=user;		DNAFLAGS="";		PROTEXT=user;		PROFLAGS=""



in:in1
informat:genbank
inmask:
insave:


item:Phylip Distance Matrix
itemmethod:(/bin/rm -f treefile infile outfile; arb_convert_aln -GenBank in1 -phylip infile ; $PREEDIT ${ARB_XCMD:-cmdtool} $DPGM;${ARB_TEXTEDIT:-textedit} outfile;/bin/rm -f in1 infile outfile)&
itemhelp:phylip.help
 
arg:DPGM
arglabel:Treat data as..
argtype:chooser
argchoice:DNA/RNA:dnadist
argchoice:AA:protdist

arg:PREEDIT
argtype:chooser
arglabel:Edit input before running?
argchoice:No:
argchoice:Yes:${ARB_TEXTEDIT:-textedit} infile;
 
in:in1
informat:genbank
inmask:
insave:


item:Phylip Parsimony/M.L.
 
itemmethod:(/bin/rm -f treefile infile outfile; arb_convert_aln -GenBank  in1  -phylip infile ;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ;/bin/rm -f  in1  infile outfile treefile  )&
itemhelp:phylip.help

arg:DISPLAY_FUNC
argtype:chooser
arglabel:What to do with the tree:?
argchoice:ARB ('tree_phylip'):arb_read_tree $CONSFLAG tree_ph_$$ treefile "PRG=$PROGRAM FILTER=$FILTER PKG=phylip"
argchoice:TextEdit:arb_textedit outfile
argchoice:Treetool:treetool treefile
 
arg:BOOTSTRP
arglabel:How many bootstraps ?
argtype:chooser
argchoice:Do not bootstrap:CONSFLAG=;arb_echo y |$PROGRAM
argchoice:10: arb_echo 1 r 10 y |seqboot ; /bin/mv -f outfile infile; arb_echo m 10 y |$PROGRAM; /bin/mv -f treefile infile;arb_echo y | consense;arb_textedit outfile
argchoice:100: arb_echo 1 r 100 y |seqboot ; /bin/mv -f outfile infile; arb_echo m 100 y |$PROGRAM; /bin/mv -f treefile infile;arb_echo y | consense;arb_textedit outfile
argchoice:1000: arb_echo 1 r 1000 y |seqboot ; /bin/mv -f outfile infile; arb_echo m 1000 y |$PROGRAM; /bin/mv -f treefile infile;arb_echo y | consense;arb_textedit outfile

arg:PROGRAM
argtype:chooser
arglabel:Which program to run?
argchoice:DNAPARS:dnapars
 
 
argchoice:DNACOMP:dnacomp
 
argchoice:DNAINVAR:dnainvar
argchoice:PROTPARS:protpars
 



in:in1
informat:genbank
inmask:
insave:


item:DNA_ML (FastDnaMl) (max 150 Species)
itemmethod:(/bin/rm -f outfile infile treefile ;echo Y F "`arb_export_rates $RATES`" |arb_convert_aln -GenBank in1 -phylip2 infile;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ; rm in1 )&
itemhelp:phylip.help

arg:RATES
argtype:weights
arglabel:Select a Weighting Mask
argchoice:POS_VAR_BY_PARS

arg:DISPLAY_FUNC
argtype:chooser
arglabel:What to do with the tree:?
argchoice:ARB ('tree_fml_//'):arb_read_tree tree_fml_$$ treefile "PRG=FASTDNAML FILTER=$FILTER PKG=olsen/felsenstein RATE=$RATES"
argchoice:Treetool:treetool treefile

in:in1
informat:genbank
inmask:
insave:


item:Protein_ML (molphy max 40 species)
 
itemmethod:(/bin/rm -f treefile infile outfile; arb_convert_aln -GenBank  in1  -phylip infile ;cat infile |tr '?' '-' >in1.in;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ;/bin/rm -f  in1  infile outfile treefile  )&
itemhelp:phylip.help

arg:DISPLAY_FUNC
argtype:chooser
arglabel:What to do with the tree:?
argchoice:ARB ('tree_phylip'):arb_read_tree $CONSFLAG tree_ph_$$ protml.tre "PRG=protml PARMETERS=$MODEL$SEARCH FILTER=$FILTER PKG=molphy"
argchoice:TextEdit:arb_textedit outfile
argchoice:Treetool:treetool treefile
 
arg:BOOTSTRP
arglabel:How many bootstraps ?
argtype:chooser
argchoice:Do not bootstrap:CONSFLAG=;protml $MODEL $SEARCH -v -I in1.in
argchoice:10: arb_echo 1 r 10 y |seqboot ; /bin/mv -f outfile infile; arb_echo m 10 y |$PROGRAM; /bin/mv -f treefile infile;arb_echo y | consense;arb_textedit outfile
argchoice:100: arb_echo 1 r 100 y |seqboot ; /bin/mv -f outfile infile; arb_echo m 100 y |$PROGRAM; /bin/mv -f treefile infile;arb_echo y | consense;arb_textedit outfile
argchoice:1000: arb_echo 1 r 1000 y |seqboot ; /bin/mv -f outfile infile; arb_echo m 1000 y |$PROGRAM; /bin/mv -f treefile infile;arb_echo y | consense;arb_textedit outfile

arg:MODEL
argtype:chooser
arglabel:Which model to use ?
argchoice:JTT:-j
argchoice:Dayhoff:-d
argchoice:mtREV24:-m
argchoice:Poisson:-p
argchoice:Jones Tayler & Thornton:-jf
argchoice:Dayhoff-F:-df
argchoice:Adachi & Hasegawa(1995):-mf

arg:SEARCH
argtype:chooser
arglabel:Search Strategie
argchoice:star decomposition:-s
argchoice:exhaustive:-e
argchoice:quickadd:-q

in:in1
informat:genbank
inmask:
insave: