#
#     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
menumeta: E

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

lmenu:Print
menumeta: r

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

lmenu:Import
menumeta:I

item:Import sequences using Readseq (slow) ...
seqtype:-
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

menu:Align
menumeta:A

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; ${ARB_XCMD:-(clustalw -output=PIR -infile=clus_in -align ; cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >out1; )tool} 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; ${ARB_XCMD:-(clustalw -output=PIR -profile1=clus_in -profile2=../clus_prf -align ; cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >out1; )tool} 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:-(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; )tool} 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/$$ ; /bin/rm -f clus_in* in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$)

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:-(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; )tool} 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/$$ ; /bin/rm -f clus_in* in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$)

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:-(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; )tool} 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/$$ ; /bin/rm -f clus_in* in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$)

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:-(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; )tool} 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/$$ ; /bin/rm -f clus_in* in1 infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$)

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

menu:User
menumeta:U

item: Start a slave ARB on a foreign host ...
seqtype:-
itemmeta: A
itemmethod:${ARB_XCMD:-(DISPLAY=$dis:0;export DISPLAY;arb_ntree :)tool} 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 ?

menu:SAI
menumeta:S

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; ${ARB_XCMD:-(cat in1.ph |arb_dnarates)tool} bash -x -c ''LD_LIBRARY_PATH="${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:

in:in1
informat:genbank
inmask:
insave:

menu:Incremental phylogeny
menumeta:c

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:-(time arb_fastdnaml $PROGRAM;$DISPLAY_FUNC)tool} 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:

menu:Phylogeny Distance Matrix
menumeta:D

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;${ARB_XCMD:-($DPGM;mv -f outfile infile;${ARB_XCMD:-cmdtool} $PROGRAM;$DISPLAY_FUNC)tool} 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:

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;${ARB_XCMD:-($CORRECTION_PROT;$CORRECTION_DNA;$PROGRAM_SEL;$DPGM;mv infile infile.1; mv -f outfile infile;arb_echo $PROGRAM_FLAGS |$PROGRAM;$DISPLAY_FUNC)tool} bash -x -c ''LD_LIBRARY_PATH="${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:-( $PREEDIT  $DPGM ; arb_textedit outfile & )tool} bash -x -c ''LD_LIBRARY_PATH="${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:

menu:Phylogeny max. parsimony
menumeta:p

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:-(arb_dnapars $BOOTSTRP $SEARCH $VIEWOUT $RANDOM $TRANSVERSION_PARS $THRESHOLD_PARS $INTERACTIVE;$DISPLAY_FUNC)tool} 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:-(arb_protpars $BOOTSTRP $GENETIC_CODE $VIEWOUT $RANDOM $THRESHOLD_PARS $INTERACTIVE;$DISPLAY_FUNC)tool} 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:

menu:Phylogeny max. Likelyhood EXP
menumeta:X

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:-(cp infile last.infile; time arb_fastdnaml $PROGRAM;$DISPLAY_FUNC)tool} 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:

menu:Phylogeny max. Likelyhood
menumeta:L

item:RAxML (DNA)
itemmethod: (mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args ; arb_export_rates -r "$RATES" > weights; arb_convert_aln -GenBank in1 -phylip2 infile; ${ARB_XCMD:-arb_raxml DNA infile weights "$TREE" $CONSTRAINT $RANDOMSTART $OPTIMIZEPARAMETERS $SEARCH "$INITIALREARRANGEMENT" "$SEED" "$NUMBEROFRUNS" "$TAKETREES" $CONSENSE $RATEMODELNUC $NUMCATEGORIES tool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; arb_raxml DNA infile weights "$TREE" $CONSTRAINT $RANDOMSTART $OPTIMIZEPARAMETERS $SEARCH "$INITIALREARRANGEMENT" "$SEED" "$NUMBEROFRUNS" "$TAKETREES" $CONSENSE $RATEMODELNUC $NUMCATEGORIES  ;arb_wait''; cd ~/.arb_tmp/$$ ; /bin/rm -f in1 last.infile treefile.in weights RAxML_info.treefile infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$ )& 
seqtype:N
itemmeta:R
itemhelp:raxml.help

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

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

arg:CONSTRAINT
argtype:choice_menu
arglabel:Use as constraint tree
argchoice:No:0
argchoice:Yes:1

arg:RANDOMSTART
argtype:choice_menu
arglabel:Generate random starting tree\n(if no tree selected)
argchoice:No:0
argchoice:Yes:1

arg:RATEMODELNUC
argtype:choice_menu
arglabel: Rate Distribution Model
argchoice:GTRMIX:GTRMIX
argchoice:GTRGAMMA:GTRGAMMA
argchoice:GTRCAT:GTRCAT
argchoice:GTRCAT_GAMMA:GTRCAT_GAMMA
argchoice:GTRGAMMAI:GTRGAMMAI
argchoice:GTRMIXI:GTRMIXI
argchoice:GTRCAT_GAMMAI:GTRCAT_GAMMAI

arg:NUMCATEGORIES
argtype:text
arglabel: # rate categories (GTRCAT only)
argtext:25

arg:OPTIMIZEPARAMETERS
argtype:choice_menu
arglabel:Optimize branches/parameters\n(GTRMIX / GTRGAMMA only)
argchoice:No:0
argchoice:Yes:1

arg:SEARCH
argtype:choice_menu
arglabel:Select RAxML algorithm
argchoice:new rapid hill climbing:d
argchoice:old hill climbing:o
argchoice:optimize input tree:e
argchoice:rapid bootstrap analysis:a
argchoice:advanced bootstrap + refinement of BS tree:i
argchoice:add new sequences to input tree (MP):p
argchoice:randomized tree searches (fixed start tree):t

arg:SEED
argtype:text
arglabel:Random seed\n(empty=use time)
argtext:

arg:INITIALREARRANGEMENT
argtype:text
arglabel:Initial rearrangement setting\n(empty=autodetect)
argtext:

arg:NUMBEROFRUNS
argtype:text
arglabel:Number of runs
argtext:1

arg:TAKETREES
argtype:text
arglabel:Select ## best trees
argtext:1

arg:CONSENSE
argtype:choice_menu
arglabel:What to do with selected trees?
argchoice:Import into ARB:import
argchoice:Create consense tree:consense

in:in1
informat:genbank
inmask:
insave:

item:RAxML (Protein)
itemmethod: (mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; /bin/rm -f nofile infile intree outfile outtree treefile arb_read_tree_args ; arb_export_rates -r "$RATES" > weights; arb_convert_aln -GenBank in1 -phylip2 infile; ${ARB_XCMD:-arb_raxml PROTEIN infile weights "$TREE" $CONSTRAINT $RANDOMSTART $OPTIMIZEPARAMETERS $SEARCH "$INITIALREARRANGEMENT" "$SEED" "$NUMBEROFRUNS" "$TAKETREES" $CONSENSE "$RATEMODELPROT" "$MATRIXNAME$EMPBFREQ" tool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; arb_raxml PROTEIN infile weights "$TREE" $CONSTRAINT $RANDOMSTART $OPTIMIZEPARAMETERS $SEARCH "$INITIALREARRANGEMENT" "$SEED" "$NUMBEROFRUNS" "$TAKETREES" $CONSENSE "$RATEMODELPROT" "$MATRIXNAME$EMPBFREQ"  ;arb_wait''; cd ~/.arb_tmp/$$ ; /bin/rm -f in1 last.infile treefile.in weights RAxML_info.treefile infile intree outfile outtree treefile arb_read_tree_args; cd .. ; rmdir $$ )& 
seqtype:A
itemmeta:P
itemhelp:raxml.help

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

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

arg:CONSTRAINT
argtype:choice_menu
arglabel:Use as constraint tree
argchoice:No:0
argchoice:Yes:1

arg:RANDOMSTART
argtype:choice_menu
arglabel:Generate random starting tree\n(if no tree selected)
argchoice:No:0
argchoice:Yes:1

arg:RATEMODELPROT
argtype:choice_menu
arglabel:Rate Distribution Model
argchoice:PROTMIX:PROTMIX
argchoice:PROTGAMMA:PROTGAMMA
argchoice:PROTCAT:PROTCAT
argchoice:PROTCAT_GAMMA:PROTCAT_GAMMA
argchoice:PROTGAMMAI:PROTGAMMAI
argchoice:PROTMIXI:PROTMIXI
argchoice:PROTCAT_GAMMAI:PROTCAT_GAMMAI

arg:MATRIXNAME
argtype:choice_menu
arglabel:AA Substitution Model
argchoice:DAYHOFF:DAYHOFF
argchoice:DCMUT:DCMUT
argchoice:JTT:JTT
argchoice:MTREV:MTREV
argchoice:WAG:WAG
argchoice:RTREV:RTREV
argchoice:CPREV:CPREV
argchoice:VT:VT
argchoice:BLOSUM62:BLOSUM62
argchoice:MTMAM:MTMAM
argchoice:GTR:GTR

arg:EMPBFREQ
arglabel:Use empirical base frequencies?
argtype:choice_menu
argchoice:No:
argchoice:Yes:F

arg:OPTIMIZEPARAMETERS
argtype:choice_menu
arglabel:Optimize branches/parameters\n(PROTMIX / PROTGAMMA only)
argchoice:No:0
argchoice:Yes:1

arg:SEARCH
argtype:choice_menu
arglabel:Select RAxML algorithm
argchoice:new rapid hill climbing:d
argchoice:old hill climbing:o
argchoice:optimize input tree:e
argchoice:rapid bootstrap analysis:a
argchoice:advanced bootstrap + refinement of BS tree:i
argchoice:add new sequences to input tree (MP):p
argchoice:randomized tree searches (fixed start tree):t

arg:SEED
argtype:text
arglabel:Random seed\n(empty=use time)
argtext:

arg:INITIALREARRANGEMENT
argtype:text
arglabel:Initial rearrangement setting\n(empty=autodetect)
argtext:

arg:NUMBEROFRUNS
argtype:text
arglabel:Number of runs
argtext:1

arg:TAKETREES
argtype:text
arglabel:Select ## best trees
argtext:1

arg:CONSENSE
argtype:choice_menu
arglabel:What to do with selected trees?
argchoice:Import into ARB:import
argchoice:Create consense tree:consense

in:in1
informat:genbank
inmask:
insave:

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:-(arb_phyml infile DNA $MODEL $OPTFREQ $BASEFREQEST $TSTVRATIO $PINVAR $INTERACTIVE; $DISPLAY_FUNC )tool} bash -x -c ''LD_LIBRARY_PATH="${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:-(arb_phyml infile AA $MODEL $PINVAR $INTERACTIVE; $DISPLAY_FUNC )tool} bash -x -c ''LD_LIBRARY_PATH="${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:-(arb_proml $BOOTSTRAP $MODEL $VIEWOUT $ANALYSIS $RANDOM $REARRANGE $RATE_VARIATION $VARIATION_COEFF $HMM_RATES $INV_FRACTION $INTERACTIVE; $DISPLAY_FUNC)tool} bash -x -c ''LD_LIBRARY_PATH="${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:

menu:Phylogeny (Other)
menumeta:O

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;${ARB_XCMD:-(puzzle;$DISPLAY_FUNC)tool} 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:

item:DeSoete Tree fit
itemmeta: S
itemmethod: (${ARB_XCMD:-(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)tool} 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

