#
#     WARNING: this file is created automatically!
#     instead edit ../../GDEHELP/ARB_GDEmenus.source
#     and *.menu in ../../GDEHELP/MENUS/ 
#     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
#

menu:Export
menumeta: E

item:Export sequences to foreign format (Readseq) ...
itemmeta: R
seqtype:*
itemmethod:arb_readseq TmpInputFile -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:filename
arglabel:Save as?

in:TmpInputFile
informat:genbank

menu:Print
menumeta: r

item:Pretty print sequences (slow) ...
itemmeta: P
seqtype:*
itemmethod: mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; (arb_readseq TmpInputFile -p -a -f=pretty $NAMELEFT $NAMERIGHT $NUMTOP $NUMBOT $NUMLEFT $NUMRIGHT -col=$COLS -width=$WIDTH $MATCH $GAPC > pretty.seq || (arb_message "Error running arb_readseq (inspect console for details)";false) ) && (arb_textprint pretty.seq; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$ )&
itemhelp:readseq.help

in:TmpInputFile
informat:genbank
insave:

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

menu:Import
menumeta:I

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

arg:INPUTFILE
argtype:filename
arglabel:Name of file to import

out:TmpOutputFile
outformat:genbank

item:Import fields from calc-sheet
itemmeta: c
itemmethod:( import_from_table.pl "$FROMFILE" --match "$MATCHCOL,$MATCHFIELD" --write "$WRITECOL,$WRITEFIELD" $SEPARATOR $OVERWRITE $SKIPUNKNOWN $MARKEDONLY $MARK $ASINT )&

arg:FROMFILE
argtype:filename
arglabel:Import from CSV
argtext:csv

arg:WRITECOL
arglabel:Write content of column
argtype:slider
argmin:1
argmax:9999

arg:WRITEFIELD
arglabel:to field
argtype:text

arg:MATCHFIELD
arglabel:of species for which field
argtype:text

arg:MATCHCOL
arglabel:matches content of column
argtype:slider
argmin:1
argmax:9999

arg:SEPARATOR
argtype:choice_menu
arglabel:Columns are separated by
argchoice:tabs:
argchoice:commas:--csv

arg:OVERWRITE
argtype:chooser
arglabel:Overwrite existing fields
argchoice:no:
argchoice:yes:--overwrite

arg:SKIPUNKNOWN
argtype:choice_menu
arglabel:Unmatched entries will  
argchoice:abort importing:
argchoice:be skipped:--skip-unknown

arg:MARKEDONLY
argtype:choice_menu
arglabel:Import to 
argchoice:all species:
argchoice:marked species:--marked-only

arg:MARK
argtype:choice_menu
arglabel:Mark
argchoice:dont change:
argchoice:species when writing field (unmark rest):--mark

arg:ASINT
arglabel:Field type
argtype:choice_menu
argchoice:Text:
argchoice:Numeric:--as-integer

menu:Align
menumeta:A

item:ProbCons
itemmeta: P
seqtype:*
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; arb_sed 's/#/>HASH_/' <TmpInputFile | arb_sed 's/%/>PERCENT_/' | arb_sed 's/"/>QUOTE_/'| arb_sed 's/@/>AT_/' | arb_sed '/^[^>]/ y/./-/' > probcons_in; ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; ($ARBHOME/bin/probcons -pre $PRE_TRAINING_REPS -ir $PASSES -c $REPS probcons_in > probcons_out;) ;arb_wait@@; arb_sed 's/>HASH_/#/' <probcons_out | arb_sed 's/>PERCENT_/%/' | arb_sed 's/>QUOTE_/"/' | arb_sed 's/>AT_/@/' > TmpOutputFile; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$ )

arg:REPS
argtype:choice_menu
arglabel:Passes of consistency transformation
argtype:slider
argmin:0
argmax:5
argvalue:2

arg:PASSES
arglabel:Passes of iterative refinement
argtype:slider
argmin:0
argmax:1000
argvalue:100

arg:PRE_TRAINING_REPS
arglabel:Rounds of pre-training before aligning the sequences
argtype:slider
argmin:0
argmax:20
argvalue:0

in:TmpInputFile
informat:flat
intyped:detailed
insave:

out:TmpOutputFile
outformat:flat

item:Muscle
itemmeta: M
seqtype:*
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; arb_sed 's/#/>HASH_/' <TmpInputFile | arb_sed 's/%/>PERCENT_/' | arb_sed 's/"/>QUOTE_/'| arb_sed 's/@/>AT_/' | arb_sed '/^[^>]/ y/./-/' > muscle_in; ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; ($ARBHOME/bin/muscle $SCORE $DIAGS $ANCHORS $DIMER $BRENNER -in muscle_in -out muscle_out -maxiters $MAXITERS;) ;arb_wait@@; arb_sed 's/>HASH_/#/' <muscle_out | arb_sed 's/>PERCENT_/%/' | arb_sed 's/>QUOTE_/"/' | arb_sed 's/>AT_/@/' > TmpOutputFile; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$)

arg:MAXITERS
argtype:text
arglabel:Maximum number of iterations to run(Use 2 for large datasets)
argtext:16

in:TmpInputFile
informat:flat
intyped:detailed
insave:

out:TmpOutputFile
outformat:flat

item:Mafft
itemmeta: f
seqtype:*
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; arb_sed 's/#/>HASH_/' <TmpInputFile | arb_sed 's/%/>PERCENT_/' | arb_sed 's/"/>QUOTE_/'| arb_sed 's/@/>AT_/' | arb_sed '/^[^>]/ y/./-/' > mafft_in; ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; ($ARBHOME/bin/$COMMAND $METHOD --preservecase --ep $OFFSET $SCORING_MATRIX mafft_in > mafft_out;) ;arb_wait@@; arb_sed 's/>HASH_/#/' <mafft_out | arb_sed 's/>PERCENT_/%/' | arb_sed 's/>QUOTE_/"/' | arb_sed 's/>AT_/@/' > TmpOutputFile; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$)

itemhelp:mafft.help

arg:COMMAND
argtype:choice_menu
arglabel:Method
argchoice:Auto:mafft --auto 
argchoice:L-INS-i:mafft-linsi
argchoice:G-INS-i:mafft-ginsi
argchoice:E-INS-i:mafft-einsi
argchoice:Q-INS-i:mafft-qinsi
argchoice:X-INS-i:mafft-xinsi
argchoice:FFT-NS-i:mafft-fftnsi
argchoice:FFT-NS-2:mafft-fftns
argchoice:NW-NS-i:mafft-nwnsi
argchoice:NW-NS-2:mafft-nwns

arg:SCORING_MATRIX
argtype:choice_menu
arglabel:Scoring matrix
argchoice:BLOSUM62:--bl 62
argchoice:BLOSUM30:--bl 30
argchoice:BLOSUM45:--bl 45
argchoice:BLOSUM80:--bl 80
argchoice:JTT100:--jtt 100
argchoice:JTT200:--jtt 200
argchoice:JTT200:--jtt 200
argchoice:1PAM / K=2:--kimura 1
argchoice:20PAM / K=2:--kimura 20
argchoice:200PAM / K=2:--kimura 200

arg:OFFSET
argtype:text
arglabel:Offset value [0..1]\n(Use Values >0.1 for closely related sequences)
argtext:0.5

in:TmpInputFile
informat:flat
intyped:detailed
insave:

out:TmpOutputFile
outformat:flat

item:ClustalW automatic
itemmeta: W
seqtype:*
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; tr '"%//' '>' <TmpInputFile >clus_in; ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${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" >TmpOutputFile; ) ;arb_wait@@; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$)

itemhelp:clustalw.help

in:TmpInputFile
informat:flat
insave:

out:TmpOutputFile
outformat:flat

item:Create ClustalW Profile 2
itemmeta: C
seqtype:*
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; tr '"%//' '>' <TmpInputFile >../clus_prf ; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$)

itemhelp:clustalw.help

in:TmpInputFile
informat:flat
insave:

item:ClustalW Profile Alignment
itemmeta: A
seqtype:*
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; tr '"%//' '>' <TmpInputFile >clus_in; ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (clustalw -output=PIR -profile1=clus_in -profile2=../clus_prf -align ; cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; ) ;arb_wait@@; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$)

itemhelp:clustalw.help

in:TmpInputFile
informat:flat
insave:

out:TmpOutputFile
outformat:flat

item:ClustalW DNA Alignment (fast)
seqtype: N
itemmeta: N
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; tr '"%//' '>' <TmpInputFile >clus_in ; ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${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=$DNAMATRIX; cat clus_in.pir | arb_sed "s/^>DL;/#/g" | arb_sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; ) ;arb_wait@@ ; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$)

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:TmpInputFile
informat:flat
insave:

out:TmpOutputFile
outformat:flat

item:ClustalW DNA Alignment (slow & accurate)
seqtype: N
itemmeta: s
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; tr '"%//' '>' <TmpInputFile >clus_in ; ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${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=$DNAMATRIX; cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; ) ;arb_wait@@ ; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$)

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:TmpInputFile
informat:flat
insave:

out:TmpOutputFile
outformat:flat

item:ClustalW Protein Alignment (fast)
seqtype: A
itemmeta: o
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; tr '"%//' '>' <TmpInputFile >clus_in ; ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${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 $NEGMATRIX; cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; ) ;arb_wait@@ ; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$)

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:TmpInputFile
informat:flat
insave:

out:TmpOutputFile
outformat:flat

item:ClustalW Protein Alignment (slow & accurate)
seqtype: A
itemmeta: l
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; tr '"%//' '>' <TmpInputFile >clus_in ; ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${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 $NEGMATRIX; cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; ) ;arb_wait@@ ; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$)

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:TmpInputFile
informat:flat
insave:

out:TmpOutputFile
outformat:flat

item:Assemble Contigs
itemmeta: g
seqtype:*
itemmethod: ( mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; tr '"%//' '>' <TmpInputFile > tr.out; CAP2 tr.out $OVERLAP $PMATCH >  TmpOutputFile; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$ )
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:TmpInputFile
informat:flat
insave:

out:TmpOutputFile
outformat:gde

menu:User
menumeta:U

item: Start a slave ARB on a foreign host ...
itemmeta: A
itemmethod:${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${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/$$; cd ~/.arb_tmp/$$ ; arb_export_rates --arb-notify "" "M $RESIDUES" "T $TTRATIO" "U" $LENGTHS "F" | arb_convert_aln --arb-notify -GenBank TmpInputFile -fastdnaml dnarates.in && ( echo 1; arb_export_tree $TREE || (arb_message "Error running arb_export_tree '$TREE' (inspect console for details)";false)  ) >>dnarates.in && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; arb_dnarates dnarates.in ;arb_wait@@; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$ )&

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:TmpInputFile
informat:genbank
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 --arb-notify "$RATES" "Y 1" "Q" "R" "G 0 0" "T 2.0" | arb_convert_aln --arb-notify -GenBank TmpInputFile -fastdnaml infile && ( arb_export_tree $TREE || (arb_message "Error running arb_export_tree '$TREE' (inspect console for details)";false) ) >>infile && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (time arb_fastdnaml $PROGRAM && $DISPLAY_FUNC) ;arb_wait@@;/bin/rm -f TmpInputFile )&
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=$FILTER RATE=$RATES PKG=olsen/felsenstein"
argchoice:Treetool:treetool treefile

in:TmpInputFile
informat:genbank
insave:

menu:Phylogeny Distance Matrix
menumeta:D

item:Phylip Distance Methods (Original Phylip, Interactive)
itemmeta: I
seqtype:*
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$;arb_convert_aln --arb-notify -GenBank TmpInputFile -phylip infile && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; ($DPGM;mv -f outfile infile;(${ARB_XCMD} $PROGRAM || (arb_message "Error running $PROGRAM (inspect console for details)";false) ) && $DISPLAY_FUNC) ;arb_wait@@;mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$)&
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:TmpInputFile
informat:genbank
insave:

item:Phylip Distance Methods (Simple GUI Based Interface)
itemmeta: G
seqtype:*
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$;arb_convert_aln --arb-notify -GenBank TmpInputFile -phylip infile && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${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 || (arb_message "Error running $PROGRAM (inspect console for details)";false) ) && $DISPLAY_FUNC) ;arb_wait@@;mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$)&
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:TmpInputFile
informat:genbank
insave:

item:Phylip Distance Matrix
itemmeta: M
seqtype:*
itemmethod: mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$;arb_convert_aln --arb-notify -GenBank TmpInputFile -phylip infile && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; ( $PREEDIT  $DPGM ; arb_textedit outfile & ) ;arb_wait@@ ; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$
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:TmpInputFile
informat:genbank
insave:

menu:Phylogeny max. parsimony
menumeta:p

item:Phylip DNAPARS
seqtype: N
itemmeta: D
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$;arb_convert_aln --arb-notify -GenBank TmpInputFile -phylip infile && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${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@@;mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$ )&
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:TmpInputFile
informat:genbank
insave:

item:Phylip PROTPARS
seqtype: A
itemmeta: P
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$;arb_convert_aln --arb-notify -GenBank TmpInputFile -phylip infile && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (arb_protpars $BOOTSTRP $GENETIC_CODE $VIEWOUT $RANDOM $THRESHOLD_PARS $INTERACTIVE && $DISPLAY_FUNC) ;arb_wait@@;mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$ )&
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:TmpInputFile
informat:genbank
insave:

menu:Phylogeny max. Likelyhood EXP
menumeta:X

item:AxML + FastdnaML
seqtype: N
itemmeta: A
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; arb_export_rates --arb-notify "$RATES" "T 2.0" "Y 1" "$QUICKADD" | arb_convert_aln --arb-notify -GenBank TmpInputFile -fastdnaml infile && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (cp infile last.infile; time arb_fastdnaml $PROGRAM && $DISPLAY_FUNC) ;arb_wait@@; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$ )&

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"
argchoice:Treetool:treetool treefile

in:TmpInputFile
informat:genbank
insave:

menu:Phylogeny max. Likelyhood
menumeta:L

item:RAxML (DNA)
itemmethod: (mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; arb_export_rates --arb-notify -r "$RATES" > weights && arb_convert_aln --arb-notify -GenBank TmpInputFile -phylip infile && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; arb_raxml DNA infile weights "$BASETREE" $CONSTRAINT $RANDOMSTART $OPTIMIZEPARAMETERS $SEARCH "$INITIALREARRANGEMENT" "$SEED" "$NUMBEROFRUNS" "$TAKETREES" $CONSENSE "PRG=RAxML FILTER=$FILTER RATE=$RATES ALGO=!$SEARCH" $RATEMODELNUC $NUMCATEGORIES  ;arb_wait@@; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$ )&
seqtype:N
itemmeta:R
itemhelp:raxml.help

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

arg:BASETREE
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:GTRGAMMA:GTRGAMMA
argchoice:GTRCAT:GTRCAT
argchoice:GTRGAMMAI:GTRGAMMAI
argchoice:GTRCATI:GTRCATI

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

arg:OPTIMIZEPARAMETERS
argtype:choice_menu
arglabel:Optimize branches/parameters\n(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: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 consensus tree:consense

in:TmpInputFile
informat:genbank
insave:

item:RAxML (Protein)
itemmethod: (mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; arb_export_rates --arb-notify -r "$RATES" > weights && arb_convert_aln --arb-notify -GenBank TmpInputFile -phylip infile && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; arb_raxml PROTEIN infile weights "$BASETREE" $CONSTRAINT $RANDOMSTART $OPTIMIZEPARAMETERS $SEARCH "$INITIALREARRANGEMENT" "$SEED" "$NUMBEROFRUNS" "$TAKETREES" $CONSENSE "PRG=RAxML FILTER=$FILTER RATE=$RATES ALGO=!$SEARCH" "$RATEMODELPROT" "$MATRIXNAME$EMPBFREQ"  ;arb_wait@@; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$ )&
seqtype:A
itemmeta:x
itemhelp:raxml.help

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

arg:BASETREE
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:PROTGAMMA:PROTGAMMA
argchoice:PROTCAT:PROTCAT
argchoice:PROTGAMMAI:PROTGAMMAI
argchoice:PROTCATI:PROTCATI

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:LG:LG
argchoice:MTART:MTART
argchoice:MTZOA:MTZOA
argchoice:PMB:PMB
argchoice:HIVB:HIVB
argchoice:HIVW:HIVW
argchoice:JTTDCMUT:JTTDCMUT
argchoice:FLU:FLU
argchoice:LG4M:LG4M
argchoice:LG4X:LG4X
argchoice:GTR:GTR
argchoice:GTR_UNLINKED:GTR_UNLINKED
argchoice:DUMMY:DUMMY
argchoice:DUMMY2:DUMMY2
argchoice:AUTO:AUTO

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(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: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 consensus tree:consense

in:TmpInputFile
informat:genbank
insave:

item: PHYML-20130708 (DNA)
seqtype: N
itemmethod:(   mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$;arb_convert_aln --arb-notify -GenBank TmpInputFile -phylip infile && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; if [ "$TREE" != "tree_?????" -a ! -z "$TREE" ]; then arb_export_tree $TREE > input_tree.in; INPUT_TREE_PARAM=-uinput_tree.in; fi; ($ARBHOME/bin/phyml_20130708 --input=infile --datatype=nt --model=$MODEL -f$BASEFREQEST --bootstrap=$BOOTSTRAP --search=$SEARCH -o$PARAM_OPTIMIZATION --r_seed=$RAND_SEED --pinv=$PROPINVAR --alpha=$ALPHA $INPUT_TREE_PARAM $CUSTOM_PARAMS || (arb_message "Error running phyml_20130708 (inspect console for details)";false) ) &&  mv infile_phyml_tree.txt outtree && $DISPLAY_FUNC ;arb_wait@@)&
itemmeta: P
itemhelp:phyml-20130708.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree?
argchoice:ARB ('tree_phyml_'):arb_read_tree tree_phyml_$$ outtree "PRG=phyml-20130708 FILTER=$FILTER STYPE=DNA"
argchoice:TextEdit:arb_textedit outfile &
argchoice:Treetool:treetool outtree

arg:MODEL
argtype:choice_menu
arglabel:Nuc. substitution model
argchoice:GTR:GTR
argchoice:HKY85 (default):HKY85
argchoice:JC69:JC69
argchoice:K80:K80
argchoice:F81:F81
argchoice:F84:F84
argchoice:TN93:TN93

arg:PARAM_OPTIMIZATION
argtype:choice_menu
arglabel:Specific parameter optimization
argchoice:Optimize tree topology, branch len, rate params:tlr
argchoice:Optimize tree topology and branch length:tl
argchoice:Optimize branch length and rate parameters:lr
argchoice:Optimize branch length:l
argchoice:Optimize rate parameters:r
argchoice:Do not optimize any parameters:n

arg:PROPINVAR
argtype:text
arglabel:Proportion of invariable sites\n(Range [0..1] or e to get the maximum likelihood estimate)
argtext:e

arg:ALPHA
argtype:text
arglabel:Distribution of the gamma distribution shape parameter\n(Positive value or e to get the maximum likelihood estimate)
argtext:e

arg:RAND_SEED
argtype:text
arglabel:Pseudo random number generator seed
argtext:424242

arg:BASEFREQEST
argtype:choice_menu
arglabel:Base frequency estimates
argchoice:Empirical:e
argchoice:ML:m

arg:BOOTSTRAP
arglabel:Bootstrap
argtype:choice_menu
argchoice:(default) approximate Bayes branch supports:-5
argchoice:neither approximate likelihood ratio test nor bootstrap values are computed:0
argchoice:approximate likelihood ratio test returning aLRT statistics:-1
argchoice:approximate likelihood ratio test returning Chi2-based parametric branch supports:-2
argchoice:SH-like branch supports alone:-4
argchoice:20 boostrap replicates:20
argchoice:50 boostrap replicates:50
argchoice:100 boostrap replicates:100
argchoice:200 boostrap replicates:200
argchoice:500 boostrap replicates:500
argchoice:1000 boostrap replicates:1000
argchoice:10000 boostrap replicates:10000

arg:SEARCH
argtype:choice_menu
arglabel:Tree topology search operation option
argchoice:NNI (default, fast):NNI
argchoice:SPR (a bit slower than NNI):SPR
argchoice:BEST (best of NNI and SPR search):BEST

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

arg:CUSTOM_PARAMS
argtype:text
arglabel: Custom parameters
argtext:

in:TmpInputFile
informat:genbank
insave:

item: PHYML-20130708 (Amino acids)
seqtype: A
itemmethod:(   mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$;arb_convert_aln --arb-notify -GenBank TmpInputFile -phylip infile && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; if [ "$TREE" != "tree_?????" -a ! -z "$TREE" ]; then arb_export_tree $TREE > input_tree.in; INPUT_TREE_PARAM=-uinput_tree.in; fi; ($ARBHOME/bin/phyml_20130708 --input=infile --datatype=aa --model=$MODEL -f$BASEFREQEST --bootstrap=$BOOTSTRAP --search=$SEARCH -o$PARAM_OPTIMIZATION --r_seed=$RAND_SEED --pinv=$PROPINVAR --alpha=$ALPHA $INPUT_TREE_PARAM $CUSTOM_PARAMS || (arb_message "Error running phyml_20130708 (inspect console for details)";false) ) &&  mv infile_phyml_tree.txt outtree && $DISPLAY_FUNC ;arb_wait@@)&
itemmeta: Y
itemhelp:phyml-20130708.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree?
argchoice:ARB ('tree_phyml_'):arb_read_tree tree_phyml_$$ outtree "PRG=phyml-20130708 FILTER=$FILTER STYPE=AA"
argchoice:TextEdit:arb_textedit outfile &
argchoice:Treetool:treetool outtree

arg:MODEL
argtype:choice_menu
arglabel:Nuc. substitution model
argchoice:LG (default):LG
argchoice:WAG:WAG
argchoice:JTT:JTT
argchoice:MtREV:MtREV
argchoice:Dayhoff:Dayhoff
argchoice:DCMut:DCMut
argchoice:RtREV:RtREV
argchoice:CpREV:CpREV
argchoice:VT:VT
argchoice:Blosum62:Blosum62
argchoice:MtMam:MtMam
argchoice:MtArt:MtArt
argchoice:HIVw:HIVw
argchoice:HIVb:HIVb

arg:PARAM_OPTIMIZATION
argtype:choice_menu
arglabel:Specific parameter optimization
argchoice:Optimize tree topology, branch len, rate params:tlr
argchoice:Optimize tree topology and branch length:tl
argchoice:Optimize branch length and rate parameters:lr
argchoice:Optimize branch length:l
argchoice:Optimize rate parameters:r
argchoice:Do not optimize any parameters:n

arg:PROPINVAR
argtype:text
arglabel:Proportion of invariable sites\n(Range [0..1] or e to get the maximum likelihood estimate)
argtext:e

arg:ALPHA
argtype:text
arglabel:Distribution of the gamma distribution shape parameter\n(Positive value or e to get the maximum likelihood estimate)
argtext:e

arg:RAND_SEED
argtype:text
arglabel:Pseudo random number generator seed
argtext:424242

arg:BASEFREQEST
argtype:choice_menu
arglabel:Base frequency estimates
argchoice:Empirical:e
argchoice:Model:m

arg:BOOTSTRAP
arglabel:Bootstrap
argtype:choice_menu
argchoice:(default) approximate Bayes branch supports:-5
argchoice:neither approximate likelihood ratio test nor bootstrap values are computed:0
argchoice:approximate likelihood ratio test returning aLRT statistics:-1
argchoice:approximate likelihood ratio test returning Chi2-based parametric branch supports:-2
argchoice:SH-like branch supports alone:-4
argchoice:20 boostrap replicates:20
argchoice:50 boostrap replicates:50
argchoice:100 boostrap replicates:100
argchoice:200 boostrap replicates:200
argchoice:500 boostrap replicates:500
argchoice:1000 boostrap replicates:1000
argchoice:10000 boostrap replicates:10000

arg:SEARCH
argtype:choice_menu
arglabel:Tree topology search operation option
argchoice:NNI (default, fast):NNI
argchoice:SPR (a bit slower than NNI):SPR
argchoice:BEST (best of NNI and SPR search):BEST

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

arg:CUSTOM_PARAMS
argtype:text
arglabel: Custom parameters
argtext:

in:TmpInputFile
informat:genbank
insave:

item:PHYML (DNA)
seqtype: N
itemmeta: M
itemmethod:( mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$;arb_convert_aln --arb-notify -GenBank TmpInputFile -phylip infile && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${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-2.4.5 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:TmpInputFile
informat:genbank
insave:

item:PHYML (Amino acids)
seqtype: A
itemmeta: L
itemmethod:( mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$;arb_convert_aln --arb-notify -GenBank TmpInputFile -phylip infile && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${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-2.4.5 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:TmpInputFile
informat:genbank
insave:

item:Phylip PROML
seqtype: A
itemmeta: O
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$;arb_convert_aln --arb-notify -GenBank TmpInputFile -phylip infile && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${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@@;mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$ )&
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:TmpInputFile
informat:genbank
insave:

menu:Phylogeny (Other)
menumeta:O

item:FastTree2 (nucleotide)
itemmeta:F
seqtype:N
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; arb_sed 's/#/>/' <TmpInputFile | arb_sed 's/%/>/' | arb_sed 's/"/>/'| arb_sed 's/@/>/' | arb_sed '/^[^>]/ y/./-/' > fasttree_in; ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; ( ($ARBHOME/bin/FastTree $FAST $MODEL -nt fasttree_in > fasttree_out || (arb_message "Error running FastTree (inspect console for details)";false) ) && $DISPLAY_FUNC) ;arb_wait@@;)&

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree?
argchoice:Load into ARB ('tree_fasttree_//'):$ARBHOME/bin/arb_read_tree tree_fasttree_$$ fasttree_out "PRG=FastTree$FAST FILTER=$FILTER MODEL=!$MODEL"
argchoice:Treetool:treetool fasttree_out

arg:FAST
argtype:choice_menu
arglabel:speed up the neighbor joining phase\n(recommended for >50,000 sequences)
argchoice:No:
argchoice:Yes:-fastest

arg:MODEL
argtype:choice_menu
arglabel:ML Model
argchoice:Jukes-Cantor:
argchoice:GTR:-gtr

in:TmpInputFile
informat:flat
insave:

item:MrBayes
itemmeta:B
seqtype:*
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; arb_convert_aln --arb-notify -GenBank TmpInputFile -NEXUS mrbayes_in && ( arb_sed -i '/LABELPOS/d' mrbayes_in     `#MrBayes does not understand the LABELPOS command, therefore it is removed.` && arb_sed -i '/EQUATE/d' mrbayes_in       `#MrBayes does not support EQUATE macros, remove them.` && arb_sed -i '/OPTIONS/,/;/d' mrbayes_in  `#MrBayes does not support the OPTIONS block, remove it. (delete everything between OPTIONS and ';')` ) && ( `# append the mrbayes command block to the nexus file`; COMMAND="begin mrbayes; set autoclose=yes nowarn=yes; lset nst=$NST rates=$RATES ngammacat=$NGAMMACAT; mcmc ngen=$NGEN nchains=$NCHAINS temp=$TEMP samplefreq=$SAMPLEFREQ burninfrac=$BURNINFRAC; sump; sumt Outputname=mrbayes_out Conformat=simple; end;" && echo $COMMAND >> mrbayes_in; ) && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; ( ($ARBHOME/bin/mb mrbayes_in || (arb_message "Error running MrBayes (inspect console for details)";false) ) && ($ARBHOME/bin/arb_nexus2newick.awk mrbayes_out.con.tre >> mr_bayes_out.newick || (arb_message "Error running arb_nexus2newick (inspect console for details)";false) ) && $DISPLAY_FUNC) ;arb_wait@@;)&

itemhelp:MrBayes.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree?
argchoice:Load into ARB ('tree_mrBayes_//'):$ARBHOME/bin/arb_read_tree tree_mrbayes_$$ mr_bayes_out.newick "PRG=MrBayes FILTER=$FILTER RATE=$RATES"
argchoice:Treetool:treetool mr_bayes_out.newick

arg:NST
argtype:choice_menu
arglabel:Number of substitution types
argchoice:6:6
argchoice:mixed:mixed
argchoice:1:1
argchoice:2:2

arg:RATES
argtype:choice_menu
arglabel:Model for among-site rate variation
argchoice:A proportion of the sites are invariable:propinv
argchoice:No rate variation across sites:equal
argchoice:Gamma-distributed rates across sites:gamma
argchoice:Autocorrelated rates across sites:adgamma
argchoice:A proportion of the sites are invariable while the rate for the remaining sites are drawn from a gamma distribution:invgamma

arg:NGAMMACAT
argtype:text
arglabel:Number of rate categories for the gamma distribution\n(Range [0 .. n])
argtext:4

arg:NGEN
argtype:text
arglabel:Number of cycles for the MCMC algorithm
argtext:100000

arg:NCHAINS
argtype:text
arglabel:Number of chains
argtext:4

arg:TEMP
argtype:text
arglabel:Temperature parameter for heating the chains
argtext:0.5

arg:SAMPLEFREQ
argtype:text
arglabel:Markov chain sample frequency
argtext:500

arg:BURNINFRAC
argtype:text
arglabel:Fraction of samples that will be discarded\nwhen convergence diagnostics are calculated [0..1]
argtext:0.25

in:TmpInputFile
informat:genbank
insave:

item:MrBayes (custom)
itemmeta:c
seqtype:*
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; arb_convert_aln --arb-notify -GenBank TmpInputFile -NEXUS mrbayes_in && ( arb_sed -i '/LABELPOS/d' mrbayes_in     `#MrBayes does not understand the LABELPOS command, therefore it is removed.` && arb_sed -i '/EQUATE/d' mrbayes_in       `#MrBayes does not support EQUATE macros, remove them.` && arb_sed -i '/OPTIONS/,/;/d' mrbayes_in  `#MrBayes does not support the OPTIONS block, remove it. (delete everything between OPTIONS and ';')` ) && ( `# append the mrbayes command block to the nexus file`; cat $COMMAND_FILE >> mrbayes_in; ) && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; ( ($ARBHOME/bin/mb mrbayes_in || (arb_message "Error running MrBayes (inspect console for details)";false) ) && ($ARBHOME/bin/arb_nexus2newick.awk mrbayes_out.con.tre >> mr_bayes_out.newick || (arb_message "Error running arb_nexus2newick (inspect console for details)";false) ) && $DISPLAY_FUNC) ;arb_wait@@)&

itemhelp:MrBayesCustom.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree?
argchoice:Load into ARB ('tree_mrBayes_//'):$ARBHOME/bin/arb_read_tree tree_mrbayes_$$ mr_bayes_out.newick "PRG=MrBayes(custom) FILTER=$FILTER RATE=$RATES"
argchoice:Treetool:treetool mr_bayes_out.newick

arg:COMMAND_FILE
argtype:filename
arglabel:MrBayes command file

in:TmpInputFile
informat:genbank
insave:

item:TREEPUZZLE ...
itemmeta: T
seqtype:*
itemmethod:(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; arb_convert_aln --arb-notify -GenBank TmpInputFile -phylip infile && ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; ((puzzle || (arb_message "Error running puzzle (inspect console for details)";false) ) && $DISPLAY_FUNC) ;arb_wait@@;mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$ )&
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:TmpInputFile
informat:genbank
insave:

item:DeSoete Tree fit
itemmeta: S
seqtype:*
itemmethod: mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$; (${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (arb_readseq -a -f8 TmpInputFile >fasta.flat;count -t $CORR fasta.flat >count.out;lsadt <count.out -seed $SEED -init $INIT -empty -99.9 > outtree;$DISPLAY_FUNC) ;arb_wait@@;mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$ )&
itemhelp:lsadt.help

in:TmpInputFile
informat:genbank
insave:

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_$$ outtree "PRG=DeSoete CORR=$CORR FILTER=$FILTER"
argchoice:TextEdit:arb_textedit outtree &
argchoice:Treetool:treetool outtree

