# 1 "ARB_GDEmenus.source"
# 1 "<built-in>"
# 1 "<command-line>"
# 1 "ARB_GDEmenus.source"
# 11 "ARB_GDEmenus.source"
# 1 "MENUS/warning.genmenu" 1






 #
 # 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
 #
# 12 "ARB_GDEmenus.source" 2

lmenu:export
# 1 "MENUS/export.genmenu" 1





item:Export sequences to foreign format (Readseq) ...
itemmeta: R
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/NEXUS:paup
argchoice:Pretty:pretty -nametop -nameleft=3 -numright -nameright -numtop

arg:OUTPUTFILE
argtype:text
arglabel:Save as?

in:in1
informat:genbank
# 15 "ARB_GDEmenus.source" 2

lmenu:pretty_print
# 1 "MENUS/pretty_print.genmenu" 1
# 10 "MENUS/pretty_print.genmenu"
item:Pretty print sequences (slow) ...
itemmeta: P
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:choice_menu
arglabel:Names at top ?
argchoice:No:
argchoice:Yes:-nametop

arg:NAMELEFT
argtype:choice_menu
arglabel:Names at left ?
argchoice:No:
argchoice:Yes:-nameleft

arg:NAMERIGHT
argtype:choice_menu
arglabel:Names at right?
argchoice:Yes:-nameright
argchoice:No:

arg:NUMTOP
argtype:choice_menu
arglabel:Numbers at top ?
argchoice:Yes:-numtop
argchoice:No:

arg:NUMBOT
argtype:choice_menu
arglabel:Numbers at tail ?
argchoice:No:
argchoice:Yes:-numbot

arg:NUMLEFT
argtype:choice_menu
arglabel:Numbers at left ?
argchoice:Yes:-numleft
argchoice:No:

arg:NUMRIGHT
argtype:choice_menu
arglabel:Numbers at right?
argchoice:Yes:-numright
argchoice:No:

arg:MATCH
argtype:choice_menu
arglabel:Show difference to current species?
argchoice:No:
argchoice:Yes:-match

arg:GAPC
argtype:choice_menu
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
# 18 "ARB_GDEmenus.source" 2

lmenu:import
# 1 "MENUS/import.genmenu" 1





item:Import sequences using Readseq (slow) ...
itemmeta: R
itemmethod:arb_readseq $INPUTFILE -a -f2 > OUTPUTFILE
itemhelp:readseq.help

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

out:OUTPUTFILE
outformat:genbank
# 21 "ARB_GDEmenus.source" 2

menu:align
# 1 "MENUS/align.genmenu" 1






item:ClustalW automatic
itemmeta: W
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args; tr '"%//' '>' <in1 >clus_in; ${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (clustalw -output=PIR -infile=clus_in -align ; cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >out1; ) ;arb_wait''; cd ~/.arb_tmp/$$ ; /bin/rm -f clus_in* in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$)





itemhelp:clustalw.help


in:in1
informat:flat
insave:

out:out1
outformat:flat



item:Create ClustalW Profile 2
itemmeta: C
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args ; tr '"%//' '>' <in1 >../clus_prf ; cd ~/.arb_tmp/$$ ; /bin/rm -f in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$)

itemhelp:clustalw.help

in:in1
informat:flat
insave:



item:ClustalW Profile Alignment
itemmeta: P
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args; tr '"%//' '>' <in1 >clus_in; ${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (clustalw -output=PIR -profile1=clus_in -profile2=../clus_prf -align ; cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >out1; ) ;arb_wait''; cd ~/.arb_tmp/$$ ; /bin/rm -f clus_in* in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$)





itemhelp:clustalw.help


in:in1
informat:flat
insave:

out:out1
outformat:flat



item:ClustalW DNA Alignment (fast)
seqtype: N
itemmeta: N
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args; tr '"%//' '>' <in1 >clus_in ; ${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (clustalw -output=PIR -infile=clus_in -align -quicktree $INTERACTIVE -ktuple=$KTUPLE -topdiags=$TOPDIAGS -window=$WINDOW -pairgap=$PAIRGAP -score=$SCORE -type=DNA -transweight=$TRANSWEIGHT -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV -dnamatrix=$DNAMATRIX; cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >out1; ) ;arb_wait'' ; cd ~/.arb_tmp/$$ ; /bin/rm -f clus_in* in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$)
# 75 "MENUS/align.genmenu"
itemhelp:clustalw.help



arg:PAIRGAP
arglabel:Gap penalty (pairwise ali)
argtype:slider
argmin:1
argmax:500
argvalue:5

arg:KTUPLE
arglabel:K-tuple size
argtype:slider
argmin:1
argmax:4
argvalue:2

arg:TOPDIAGS
arglabel:No. of top diagonals
argtype:slider
argmin:1
argmax:50
argvalue:4

arg:WINDOW
arglabel:Window size
argtype:slider
argmin:1
argmax:50
argvalue:4



arg:DNAMATRIX
argtype:choice_menu
arglabel:Weighting matrix (multiple ali)
argchoice:IUB:IUB
argchoice:CLUSTALW:CLUSTALW

arg:GOP
argtype:slider
arglabel:Gap Open Penalty
argmin:0
argmax:100
argvalue:15

arg:GEP
arglabel:Gap Extend Penalty
argtype:slider
argmin:0
argmax:10
argvalue:6.66

arg:MAXDIV
arglabel:% identity for delay
argtype:slider
argmin:0
argmax:100
argvalue:30

arg:TRANSWEIGHT
arglabel:Transition weight
argtype:slider
argmin:0.0
argmax:1.0
argvalue:0.5

arg:INTERACTIVE
arglabel:Interactive
argtype:choice_menu
argchoice:No:
argchoice:Yes:-interactive

in:in1
informat:flat
insave:

out:out1
outformat:flat



item:ClustalW DNA Alignment (slow & accurate)
seqtype: N
itemmeta: s
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args; tr '"%//' '>' <in1 >clus_in ; ${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (clustalw -output=PIR -infile=clus_in -align $INTERACTIVE -pwdnamatrix=$PWDNAMATRIX -pwgapopen=$PWGOP -pwgapext=$PWGEP -type=DNA -transweight=$TRANSWEIGHT -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV -dnamatrix=$DNAMATRIX; cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >out1; ) ;arb_wait'' ; cd ~/.arb_tmp/$$ ; /bin/rm -f clus_in* in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$)
# 173 "MENUS/align.genmenu"
itemhelp:clustalw.help



arg:PWDNAMATRIX
argtype:choice_menu
arglabel:Weighting matrix (pairwise ali)
argchoice:IUB:IUB
argchoice:CLUSTALW:CLUSTALW

arg:PWGOP
argtype:slider
arglabel:Gap Open Penalty
argmin:0
argmax:100
argvalue:15

arg:PWGEP
arglabel:Gap Extend Penalty
argtype:slider
argmin:0
argmax:10
argvalue:6.66



arg:DNAMATRIX
argtype:choice_menu
arglabel:Weighting matrix (multiple ali)
argchoice:IUB:IUB
argchoice:CLUSTALW:CLUSTALW

arg:GOP
argtype:slider
arglabel:Gap Open Penalty
argmin:0
argmax:100
argvalue:15

arg:GEP
arglabel:Gap Extend Penalty
argtype:slider
argmin:0
argmax:10
argvalue:6.66

arg:MAXDIV
arglabel:% identity for delay
argtype:slider
argmin:0
argmax:100
argvalue:30

arg:TRANSWEIGHT
arglabel:Transition weight
argtype:slider
argmin:0.0
argmax:1.0
argvalue:0.5

arg:INTERACTIVE
arglabel:Interactive
argtype:choice_menu
argchoice:No:
argchoice:Yes:-interactive

in:in1
informat:flat
insave:

out:out1
outformat:flat



item:ClustalW Protein Alignment (fast)
seqtype: A
itemmeta: o
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args; tr '"%//' '>' <in1 >clus_in ; ${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (clustalw -output=PIR -infile=clus_in -align -quicktree $INTERACTIVE -ktuple=$KTUPLE -topdiags=$TOPDIAGS -window=$WINDOW -pairgap=$PAIRGAP -score=$SCORE -type=PROTEIN -transweight=$TRANSWEIGHT -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV -matrix=$MATRIX $NEGMATRIX; cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >out1; ) ;arb_wait'' ; cd ~/.arb_tmp/$$ ; /bin/rm -f clus_in* in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$)
# 264 "MENUS/align.genmenu"
itemhelp:clustalw.help



arg:PAIRGAP
arglabel:Gap penalty (pairwise ali)
argtype:slider
argmin:1
argmax:500
argvalue:3

arg:KTUPLE
arglabel:K-tuple size
argtype:slider
argmin:1
argmax:2
argvalue:1

arg:TOPDIAGS
arglabel:No. of top diagonals
argtype:slider
argmin:1
argmax:50
argvalue:5

arg:WINDOW
arglabel:Window size
argtype:slider
argmin:1
argmax:50
argvalue:5



arg:MATRIX
argtype:choice_menu
arglabel:Weighting matrix (multiple ali)
argchoice:Gonnet series:GONNET
argchoice:Blosum series:BLOSUM
argchoice:PAM series:PAM
argchoice:ID matrix:ID

arg:GOP
argtype:slider
arglabel:Gap Open Penalty
argmin:0
argmax:100
argvalue:10

arg:GEP
arglabel:Gap Extend Penalty
argtype:slider
argmin:0
argmax:10
argvalue:0.2

arg:MAXDIV
arglabel:% identity for delay
argtype:slider
argmin:0
argmax:100
argvalue:30

arg:TRANSWEIGHT
arglabel:Transition weight
argtype:slider
argmin:0.0
argmax:1.0
argvalue:0.5

arg:NEGMATRIX
arglabel:Use negative matrix
argtype:choice_menu
argchoice:No:
argchoice:Yes:-negative

arg:INTERACTIVE
arglabel:Interactive
argtype:choice_menu
argchoice:No:
argchoice:Yes:-interactive

in:in1
informat:flat
insave:

out:out1
outformat:flat



item:ClustalW Protein Alignment (slow & accurate)
seqtype: A
itemmeta: l
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args; tr '"%//' '>' <in1 >clus_in ; ${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (clustalw -output=PIR -infile=clus_in -align $INTERACTIVE -pwmatrix=$PWMATRIX -pwgapopen=$PWGOP -pwgapext=$PWGEP -type=PROTEIN -transweight=$TRANSWEIGHT -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV -matrix=$MATRIX $NEGMATRIX; cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >out1; ) ;arb_wait'' ; cd ~/.arb_tmp/$$ ; /bin/rm -f clus_in* in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$)
# 370 "MENUS/align.genmenu"
itemhelp:clustalw.help



arg:PWMATRIX
argtype:choice_menu
arglabel:Weighting matrix (pairwise ali)
argchoice:Gonnet series:GONNET
argchoice:Blosum series:BLOSUM
argchoice:PAM series:PAM
argchoice:ID matrix:ID

arg:PWGOP
argtype:slider
arglabel:Gap Open Penalty
argmin:0
argmax:100
argvalue:10

arg:PWGEP
arglabel:Gap Extend Penalty
argtype:slider
argmin:0
argmax:10
argvalue:0.1



arg:MATRIX
argtype:choice_menu
arglabel:Weighting matrix (multiple ali)
argchoice:Gonnet series:GONNET
argchoice:Blosum series:BLOSUM
argchoice:PAM series:PAM
argchoice:ID matrix:ID

arg:GOP
argtype:slider
arglabel:Gap Open Penalty
argmin:0
argmax:100
argvalue:10

arg:GEP
arglabel:Gap Extend Penalty
argtype:slider
argmin:0
argmax:10
argvalue:0.2

arg:MAXDIV
arglabel:% identity for delay
argtype:slider
argmin:0
argmax:100
argvalue:30

arg:TRANSWEIGHT
arglabel:Transition weight
argtype:slider
argmin:0.0
argmax:1.0
argvalue:0.5

arg:NEGMATRIX
arglabel:Use negative matrix
argtype:choice_menu
argchoice:No:
argchoice:Yes:-negative

arg:INTERACTIVE
arglabel:Interactive
argtype:choice_menu
argchoice:No:
argchoice:Yes:-interactive

in:in1
informat:flat
insave:

out:out1
outformat:flat



item:Assemble Contigs
itemmeta: g
itemmethod: ( mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args; tr '"%//' '>' <in1 >in1.tmp; CAP2 in1.tmp $OVERLAP $PMATCH > out1; cd ~/.arb_tmp/$$ ; /bin/rm -f in1 in1.tmp infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$ )



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
# 24 "ARB_GDEmenus.source" 2

menu:user
# 1 "MENUS/start_arb.genmenu" 1





item: Start a slave ARB on a foreign host ...
itemmeta: A
itemmethod:${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (DISPLAY=$dis:0;export DISPLAY;arb_ntree :) ;arb_wait'' &

arg:dis
argtype:text
arglabel:hostname of slave host ?
# 27 "ARB_GDEmenus.source" 2

menu:SAI
# 1 "MENUS/dnamlrates.genmenu" 1





item:Positional Variability by Olsons dnamlrates (max 5000 Species, 8000 seqlength)
seqtype: N
itemmeta: O
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args ; arb_export_rates "" "M $RESIDUES" "T $TTRATIO" "U" $LENGTHS "F" | arb_convert_aln -GenBank in1 -phylip2 in1.ph; echo 1 >>in1.ph; arb_export_tree $TREE >>in1.ph; ${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (cat in1.ph |arb_dnarates) ;arb_wait''; cd ~/.arb_tmp/$$ ; /bin/rm -f in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$ )&







itemhelp:DNAml_rates.help

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

arg:RESIDUES
argtype:text
arglabel:Number of informative residues
argtext:10

arg:TTRATIO
argtype:text
arglabel:Transition/transversion ratio
argtext:2.0

arg:LENGTHS
argtype:choice_menu
arglabel:Use branchlengths?
argchoice:Yes:"L"
argchoice:No:
# 51 "MENUS/dnamlrates.genmenu"
in:in1
informat:genbank
inmask:
insave:
# 30 "ARB_GDEmenus.source" 2

menu:Incremental phylogeny
# 1 "MENUS/inc_fastdnaml.genmenu" 1





item:AxML + FastdnaML (max 500 Species) ...
seqtype: N
itemmeta: M
itemmethod:(/bin/rm -f outfile infile treefile ;arb_export_rates "$RATES" "Y 1" "Q" "R" "G 0 0" "T 2.0" | arb_convert_aln -GenBank in1 -phylip2 infile;arb_export_tree $TREE >>infile;${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (time arb_fastdnaml $PROGRAM;$DISPLAY_FUNC) ;arb_wait'';rm in1 )&






itemhelp:dnaml.help

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

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

arg:PROGRAM
argtype:choice_menu
arglabel:Select program to use
argchoice:AxML:axml
argchoice:FastdnaML:fastdnaml

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


in:in1
informat:genbank
inmask:
insave:
# 33 "ARB_GDEmenus.source" 2

menu:Phylogeny_DistMatrix
# 1 "MENUS/phylip_dist_org.genmenu" 1





item:Phylip Distance Methods (Original Phylip, Interactive)
itemmeta: I
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args ; arb_convert_aln -GenBank in1 -phylip infile;${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; ($DPGM;mv -f outfile infile;${ARB_XCMD:-cmdtool} $PROGRAM;$DISPLAY_FUNC) ;arb_wait'';cd ~/.arb_tmp/$$ ; /bin/rm -f in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$)&





itemhelp:phylip_distance.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree:?
argchoice:ARB ('tree_ph_xxx'):(arb_read_tree tree_ph_$$ outtree "PRG=$PROGRAM FILTER=$FILTER PKG=phylip (Interactive)")
argchoice:TextEdit:arb_textedit outtree
argchoice:Treetool:treetool outtree

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

arg:DPGM
arglabel:Treat data as..
argtype:choice_menu
argchoice:RNA/DNA (dnadist):dnadist
argchoice:AA (protdist):protdist


in:in1
informat:genbank
inmask:sdfgdfg
insave:
# 36 "ARB_GDEmenus.source" 2
# 1 "MENUS/phylip_dist.genmenu" 1





item:Phylip Distance Methods (Simple GUI Based Interface)
itemmeta: G
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args ; arb_convert_aln -GenBank in1 -phylip infile;${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; ($CORRECTION_PROT;$CORRECTION_DNA;$PROGRAM_SEL;$DPGM;mv infile infile.1; mv -f outfile infile;arb_echo $PROGRAM_FLAGS |$PROGRAM;$DISPLAY_FUNC) ;arb_wait'';cd ~/.arb_tmp/$$ ; /bin/rm -f in1 infile.1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$)&







itemhelp:phylip_distance.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree:?
argchoice:ARB ('tree_ph_'):($CORRECTION_PROT;$CORRECTION_DNA;$PROGRAM_SEL;echo||$DPGM;arb_read_tree tree_ph_$$ outtree "PRG=$PROGRAM_NAME CORR=$TEXT FILTER=$FILTER PKG=phylip")
argchoice:TextEdit:arb_textedit outfile &
argchoice:Treetool:treetool outtree

arg:PROGRAM_SEL
arglabel:Which method?
argtype:choice_menu
argchoice:Neighbor: PROGRAM=neighbor; PROGRAM_FLAGS="y"; PROGRAM_NAME=neighbor
argchoice:UPGMA: PROGRAM=neighbor; PROGRAM_FLAGS="n y"; PROGRAM_NAME=UPGMA
argchoice:Fitch: PROGRAM=fitch; PROGRAM_FLAGS="y"; PROGRAM_NAME=fitch
argchoice:Kitsch: PROGRAM=kitsch; PROGRAM_FLAGS="y"; PROGRAM_NAME=kitsch

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

arg:CORRECTION_DNA
arglabel:Correction (DNA)
argtype:choice_menu
argchoice:F84: DNATEXT=F84; DNAFLAGS="y"
argchoice:Kimura 2-parameter: DNATEXT=Kimura; DNAFLAGS="d y"
argchoice:Jukes-Cantor: DNATEXT=Jukes-Cantor; DNAFLAGS="d d y"




arg:CORRECTION_PROT
arglabel:Correction (PROT)
argtype:choice_menu
argchoice:Jones-Taylor-Thornton: PROTEXT=JTT; PROFLAGS="y"
argchoice:Dayhoff PAM matrix: PROTEXT=Dayhoff; PROFLAGS="p y"
argchoice:Kimura formula: PROTEXT=Kimura; PROFLAGS="p p y"
argchoice:Manual: PROTEXT=User; PROFLAGS=""

in:in1
informat:genbank
inmask:
insave:



item:Phylip Distance Matrix
itemmeta: M
itemmethod: mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args ; arb_convert_aln -GenBank in1 -phylip infile ; ${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; ( $PREEDIT $DPGM ; arb_textedit outfile & ) ;arb_wait'' ; cd ~/.arb_tmp/$$ ; /bin/rm -f in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$




itemhelp:phylip_distance.help

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

arg:PREEDIT
argtype:choice_menu
arglabel:Edit input before running?
argchoice:No:
argchoice:Yes:arb_textedit infile ;

in:in1
informat:genbank
inmask:
insave:
# 37 "ARB_GDEmenus.source" 2

menu:Phylogeny_MaxParsimony
# 1 "MENUS/phylip_pars.genmenu" 1





item:Phylip DNAPARS
seqtype: N
itemmeta: D
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args ; arb_convert_aln -GenBank in1 -phylip infile;${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (arb_dnapars $BOOTSTRP $SEARCH $VIEWOUT $RANDOM $TRANSVERSION_PARS $THRESHOLD_PARS $INTERACTIVE;$DISPLAY_FUNC) ;arb_wait'';cd ~/.arb_tmp/$$ ; /bin/rm -f in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$ )&


itemhelp:dnapars.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree:?
argchoice:ARB ('tree_ph_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_ph_$$ outtree "PRG=dnapars FILTER=$FILTER PKG=phylip BOOT=$BOOTSTRP"
argchoice:TextEdit:arb_textedit outfile &
argchoice:Treetool:treetool outtree

arg:SEARCH
argtype:choice_menu
arglabel:Search depth
argchoice:More thorough search:0
argchoice:Less thorough search:1
argchoice:Rearrange on one best tree:2

arg:RANDOM
argtype:choice_menu
arglabel:Randomize sequence order
argchoice:Yes:1
argchoice:No:0

arg:TRANSVERSION_PARS
argtype:choice_menu
arglabel:Use transversion parsimony?
argchoice:No:0
argchoice:Yes:1

arg:THRESHOLD_PARS
argtype:text
arglabel:Use threshold parsimony (0=no)
argtext:0

arg:BOOTSTRP
argtype:choice_menu
arglabel:How many bootstraps ?
argchoice:Do not bootstrap:0
argchoice:10:10
argchoice:100:100
argchoice:500:500
argchoice:1000:1000
argchoice:5000:5000
argchoice:10000:10000

arg:VIEWOUT
argtype:choice_menu
arglabel:View report
argchoice:No:0
argchoice:Yes:1

arg:INTERACTIVE
argtype:choice_menu
arglabel:Interactive? (no for bootstrap)
argchoice:No:0
argchoice:Yes:1

in:in1
informat:genbank
inmask:
insave:



item:Phylip PROTPARS
seqtype: A
itemmeta: P
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args ; arb_convert_aln -GenBank in1 -phylip infile;${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (arb_protpars $BOOTSTRP $GENETIC_CODE $VIEWOUT $RANDOM $THRESHOLD_PARS $INTERACTIVE;$DISPLAY_FUNC) ;arb_wait'';cd ~/.arb_tmp/$$ ; /bin/rm -f in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$ )&


itemhelp:protpars.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree:?
argchoice:ARB ('tree_ph_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_ph_$$ outtree "PRG=protpars FILTER=$FILTER PKG=phylip BOOT=$BOOTSTRP CODE=$GENETIC_CODE"
argchoice:TextEdit:arb_textedit outfile &
argchoice:Treetool:treetool outtree

arg:GENETIC_CODE
argtype:choice_menu
arglabel:Genetic code
argchoice:Universal:U
argchoice:Mitochondrial:M
argchoice:Vertebrate mitochondrial:V
argchoice:Fly mitochondrial:F
argchoice:Yeast mitochondrial:Y

arg:RANDOM
argtype:choice_menu
arglabel:Randomize sequence order
argchoice:Yes:1
argchoice:No:0

arg:THRESHOLD_PARS
argtype:text
arglabel:Use threshold parsimony (0=no)
argtext:0

arg:BOOTSTRP
argtype:choice_menu
arglabel:How many bootstraps ?
argchoice:Do not bootstrap:0
argchoice:10:10
argchoice:100:100
argchoice:500:500
argchoice:1000:1000
argchoice:5000:5000
argchoice:10000:10000

arg:VIEWOUT
argtype:choice_menu
arglabel:View report
argchoice:No:0
argchoice:Yes:1

arg:INTERACTIVE
argtype:choice_menu
arglabel:Interactive? (no for bootstrap)
argchoice:No:0
argchoice:Yes:1

in:in1
informat:genbank
inmask:
insave:
# 40 "ARB_GDEmenus.source" 2

menu:Phylogeny_MaxLikelyhood
# 1 "MENUS/fastdnaml.genmenu" 1





item:AxML + FastdnaML
seqtype: N
itemmeta: A
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args ; arb_export_rates "$RATES" "T 2.0" "Y 1" "$QUICKADD" | arb_convert_aln -GenBank in1 -phylip2 infile; ${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (cp infile last.infile; time arb_fastdnaml $PROGRAM;$DISPLAY_FUNC) ;arb_wait''; cd ~/.arb_tmp/$$ ; /bin/rm -f in1 last.infile infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$ )&






itemhelp:dnaml.help

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

arg:PROGRAM
argtype:choice_menu
arglabel:Select program to use
argchoice:AxML:axml
argchoice:FastdnaML:fastdnaml

arg:QUICKADD
argtype:choice_menu
arglabel:Use Quickadd
argchoice:Yes:
argchoice:No:Q

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree:?
argchoice:ARB ('tree_fml_//'):arb_read_tree tree_fml_$$ treefile "PRG=$PROGRAM FILTER=$FILTER RATE=$RATES"3
argchoice:Treetool:treetool treefile

in:in1
informat:genbank
inmask:
insave:
# 43 "ARB_GDEmenus.source" 2
# 1 "MENUS/raxml.genmenu" 1





item:RAxML
itemmeta: R
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args ; arb_export_rates "$RATES" "$QUICKADD" | arb_convert_aln -GenBank in1 -phylip2 infile; ${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (cp infile last.infile; time raxml -f $SEARCH -g $NUMOFMOVE -d $STARTTEMP -l $TIMELIMIT -r $MINREARRANG -k $MAXREARRANG -m $MODELOFNUCSUB -c $NUMOFCAT -s infile -n treefile; cp RAxML_parsimonyTree.treefile treefile; $DISPLAY_FUNC) ;arb_wait'';cd ~/.arb_tmp/$$ ; /bin/rm -f in1 last.infile infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$ )&
# 19 "MENUS/raxml.genmenu"
itemhelp:dnaml.help

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

arg:SEARCH
argtype:choice_menu
arglabel:Select search algorithm
argchoice:normal hill-climbing:c
argchoice:evaluate:e
argchoice:fast:f
argchoice:simulates annealing:s

arg:TIMELIMIT
argtype:text
arglabel:Time limit for searching in sec
argtext:120

arg:NUMOFMOVE
argtype:text
arglabel:Number of moves
argtext:10

arg:STARTTEMP
argtype:text
arglabel:Start temperature for chain
argtext:3.0


arg:MODELOFNUCSUB
argtype:choice_menu
arglabel:Model of Nucleotide Substitution
argchoice:HKY85:HKY85
argchoice:HKY85CAT:HKY85CAT
argchoice:GTR:GTR
argchoice:GTRCAT:GTRCAT

arg:NUMOFCAT
argtype:text
arglabel:Number of distinct rate categories for raxml
argtext:50

arg:MINREARRANG
argtype:text
arglabel:Minimum rearrangement setting
argtext:5

arg:MAXREARRANG
argtype:text
arglabel:Maximum rearrangement setting
argtext:21







arg:QUICKADD
argtype:choice_menu
arglabel:Use Quickadd
argchoice:Yes:
argchoice:No:Q

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree:?
argchoice:ARB ('tree_raxml_//'):arb_read_tree tree_raxml_$$ treefile "PRG=raxml FILTER=$FILTER RATE=$RATES"
argchoice:Treetool:treetool treefile

in:in1
informat:genbank
inmask:
insave:
# 44 "ARB_GDEmenus.source" 2
# 1 "MENUS/phylip_ml.genmenu" 1






item:PHYML (DNA)
seqtype: N
itemmeta: D
itemmethod:( mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args ; arb_convert_aln -GenBank in1 -phylip infile; ${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (arb_phyml infile DNA $MODEL $OPTFREQ $BASEFREQEST $TSTVRATIO $PINVAR $INTERACTIVE; $DISPLAY_FUNC ) ;arb_wait''; )&



itemhelp:phyml.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree:?
argchoice:ARB ('tree_phyml_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_phyml_$$ outtree "PRG=phyml FILTER=$FILTER STYPE=DNA"
argchoice:TextEdit:arb_textedit outfile &
argchoice:Treetool:treetool outtree

arg:MODEL
argtype:choice_menu
arglabel:Nuc. substitution model
argchoice:HKY:0
argchoice:F84:1
argchoice:TN93:2
argchoice:GTR:3
argchoice:custom:4
argchoice:JC69:5
argchoice:KP2:6
argchoice:F81:7

arg:OPTFREQ
argtype:choice_menu
arglabel:Optimize equilibrium freq.? [custom]
argchoice:No:0
argchoice:Yes:1

arg:BASEFREQEST
argtype:choice_menu
arglabel:Base frequency estimates
argchoice:empirical:0
argchoice:ML:1

arg:TSTVRATIO
argtype:choice_menu
arglabel:Ts/tv ratio
argchoice:fixed (4.00):0
argchoice:estimated:1

arg:PINVAR
argtype:choice_menu
arglabel:Proportion of invariable sites
argchoice:fixed (0.00):0
argchoice:estimated:1

arg:INTERACTIVE
argtype:choice_menu
arglabel:Interactive?
argchoice:No:0
argchoice:Yes:1

in:in1
informat:genbank
inmask:
insave:



item:PHYML (Amino acids)
seqtype: A
itemmeta: M
itemmethod:( mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args ; arb_convert_aln -GenBank in1 -phylip infile; ${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (arb_phyml infile AA $MODEL $PINVAR $INTERACTIVE; $DISPLAY_FUNC ) ;arb_wait''; )&



itemhelp:phyml.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree:?
argchoice:ARB ('tree_phyml_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_phyml_$$ outtree "PRG=phyml FILTER=$FILTER STYPE=AA"
argchoice:TextEdit:arb_textedit outfile &
argchoice:Treetool:treetool outtree

arg:MODEL
argtype:choice_menu
arglabel:AA substitution model
argchoice:JTT:0
argchoice:MtRev:1
argchoice:WAG:2
argchoice:DCMut:3
argchoice:RtREV:4
argchoice:CpREV:5
argchoice:VT:6
argchoice:Blosum62:7
argchoice:MtMam:8
argchoice:Dayhoff:9

arg:PINVAR
argtype:choice_menu
arglabel:Proportion of invariable sites
argchoice:fixed (0.00):0
argchoice:estimated:1

arg:INTERACTIVE
argtype:choice_menu
arglabel:Interactive?
argchoice:No:0
argchoice:Yes:1

in:in1
informat:genbank
inmask:
insave:



item:Phylip PROML
seqtype: A
itemmeta: O
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args ; arb_convert_aln -GenBank in1 -phylip infile;${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (arb_proml $BOOTSTRAP $MODEL $VIEWOUT $ANALYSIS $RANDOM $REARRANGE $RATE_VARIATION $VARIATION_COEFF $HMM_RATES $INV_FRACTION $INTERACTIVE; $DISPLAY_FUNC) ;arb_wait'';cd ~/.arb_tmp/$$ ; /bin/rm -f in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$ )&




itemhelp:proml.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree:?
argchoice:ARB ('tree_proml_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_proml_$$ outtree "PRG=proml FILTER=$FILTER PKG=phylip BOOT=$BOOTSTRAP MODEL=$MODEL ANALYSIS=$ANALYSIS"
argchoice:TextEdit:arb_textedit outfile &
argchoice:Treetool:treetool outtree

arg:MODEL
argtype:choice_menu
arglabel:Model
argchoice:Jones-Taylor-Thornton:JTT
argchoice:Dayhoff PAM:PAM

arg:ANALYSIS
argtype:choice_menu
arglabel:Analysis
argchoice:Rough & fast:rough
argchoice:Fine & slow:fine

arg:REARRANGE
argtype:choice_menu
arglabel:Global rearrangements
argchoice:No:0
argchoice:Yes:1

arg:RANDOM
argtype:choice_menu
arglabel:Randomize sequence order
argchoice:Yes:1
argchoice:No:0

arg:RATE_VARIATION
argtype:choice_menu
arglabel:Rate variation among sites?
argchoice:Constant rate of change:0
argchoice:Gamma distributed rates:1
argchoice:Gamma+Invariant sites:2

arg:VARIATION_COEFF
argtype:text
arglabel:Variation coeff. (gamma only)
argtext:4

arg:HMM_RATES
argtype:text
arglabel:Rates in HMM (gamma only)
argtext:4

arg:INV_FRACTION
argtype:text
arglabel:Fraction of invariant sites
argtext:0.1

arg:BOOTSTRAP
argtype:choice_menu
arglabel:How many bootstraps ?
argchoice:Do not bootstrap:0
argchoice:10:10
argchoice:100:100
argchoice:500:500
argchoice:1000:1000
argchoice:5000:5000
argchoice:10000:10000

arg:VIEWOUT
argtype:choice_menu
arglabel:View report
argchoice:No:0
argchoice:Yes:1

arg:INTERACTIVE
argtype:choice_menu
arglabel:Interactive? (no for bootstrap)
argchoice:No:0
argchoice:Yes:1

in:in1
informat:genbank
inmask:
insave:
# 45 "ARB_GDEmenus.source" 2
# 1 "MENUS/molphy.genmenu" 1





item:Protein_ML (molphy; max 40 species)
seqtype: A
itemmeta: L
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args ; arb_convert_aln -GenBank in1 -phylip infile;cat infile |tr '?' '-' >in1.in;mv in1.in infile;${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (arb_protml $MODEL $SEARCH $REARRANGE $CALCLENGTH infile ;(test -f treefile && $DISPLAY_FUNC)) ;arb_wait'';cd ~/.arb_tmp/$$ ; /bin/rm -f in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$)&





itemhelp:protml.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree:?
argchoice:ARB ('tree_protml_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_protml_$$ treefile "PRG=protml MODEL=$MODEL SEARCH=$SEARCH FILTER=$FILTER REARRANGE=$REARRANGE PKG=molphy"
argchoice:TextEdit:arb_textedit treefile &
argchoice:Treetool:treetool treefile

arg:MODEL
argtype:choice_menu
arglabel:Which model to use ?
argchoice:JTT:-j
argchoice:Dayhoff:-d
argchoice:mtREV24:-m
argchoice:Poisson:-p
argchoice:JTT-F:-jf
argchoice:Dayhoff-F:-df
argchoice:mtREV24-F:-mf
argchoice:Proportional:-pf

arg:SEARCH
argtype:choice_menu
arglabel:Search strategy
argchoice:Star decomposition:-s
argchoice:Exhaustive:-e
argchoice:Quick add:-q

arg:CALCLENGTH
argtype:choice_menu
arglabel:Calc branchlengths?
argchoice:Yes:1
argchoice:No:0

arg:REARRANGE
argtype:choice_menu
arglabel:Rearrangement
argchoice:None:0
argchoice:local Rearrangement search:-R
argchoice:LBP only:-RX

in:in1
informat:genbank
inmask:
insave:
# 46 "ARB_GDEmenus.source" 2

menu:Phylogeny_Other
# 1 "MENUS/puzzle.genmenu" 1





item:TREEPUZZLE ...
itemmeta: T
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args; arb_convert_aln -GenBank in1 -phylip2 infile;${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (puzzle;$DISPLAY_FUNC) ;arb_wait'';cd ~/.arb_tmp/$$ ; /bin/rm -f in1 outdist infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$ )&



itemhelp:treepuzzle.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree:?
argchoice:ARB ('tree_puz_//'):arb_read_tree tree_puz_$$ outtree "PRG=PUZZLE FILTER=$FILTER PKG=strimmer/v. haeseler"
argchoice:Treetool:treetool outtree

in:in1
informat:genbank
inmask:
insave:
# 49 "ARB_GDEmenus.source" 2
# 1 "MENUS/desoete.genmenu" 1





item:DeSoete Tree fit
itemmeta: S
itemmethod: (${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (arb_readseq -a -f8 in1>in1.flat;count -t $CORR in1.flat> in1.tmp;lsadt<in1.tmp -seed $SEED -init $INIT -empty -99.9 > in1.out;$DISPLAY_FUNC) ;arb_wait'';/bin/rm -f in1* )&




itemhelp:lsadt.help

in:in1
informat:genbank
insave:
inmask:

arg:CORR
arglabel:Dist. correction?
argtype:choice_menu
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:choice_menu
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 in1.out &
argchoice:Treetool:treetool in1.out
# 50 "ARB_GDEmenus.source" 2
