#-------------------- DNA distance methods  ( 6/ 3/2006) ------------------
item:DNA Distance methods
# sed edits out ":CDS" that is added by FEATURES
itemmethod:tr "~" "-" < in1 | sed "s/[\:\_]CDS/_/" | readseq -a -f12 -pipe | sed "s/ YF//1" > in1.tmp; rm in1; (dnadist.csh in1.tmp $DMETHOD $TRANSRATIO $METHOD $BSEED $REPLICATES $BLOCKSIZE $PERCENT $TCONMETH $POWER $SUBREP $GLOBAL $NEGBRANCH $OUTGRP $JUMBLE $JSEED $NUMJUM $TERMOUT $PRINTDATA in1.outfile in1.outtree; rm in1.tmp; $WHERE) &
itemhelp:doc/Phylip/dnadist.html
itemopen:gde_help_viewer.csh
 
arg:DMETHOD
argtype:choice_menu
arglabel:DISTANCE MATRIX METHOD
argchoice:F84:f
argchoice:Kimura 2-parameter:k
argchoice:Jukes-Cantor:j
argchoice:Log of the determinant:l
argvalue:0  

arg:TRANSRATIO
arglabel:TRANSITION/TRANSVERSION RATIO
argtype:slider
argmin:1
argmax:20
argvalue:2

arg:METHOD
argtype:choice_menu
arglabel:RESAMPLING (SLOW!)
argchoice:none:n
argchoice:Bootstrap:b
argchoice:Delete-half jackinfe:d
argchoice:Permute species for each character:ps
argchoice:Permute character order:po
argchoice:Permute within species:pw
argvalue:0   

arg:BSEED
argtype:slider
arglabel:_____Bootstrap random number seed
argmin:5
argmax:65535
argvalue:12345

arg:REPLICATES
argtype:slider
arglabel:_____Number of bootstrap replicates?
argmin:1
argmax:1000
argvalue:100

arg:BLOCKSIZE
argtype:slider
arglabel:_____Block size (Bootstrap only)
argmin:1
argmax:50
argvalue:1

arg:PERCENT
argtype:slider
arglabel:_____Percent of sites to sample
argmin:1
argmax:100
argvalue:100

arg:TCONMETH
arglabel:TREE CONSTRUCTION METHOD
argtype:choice_menu
argchoice:Weighbor, weighted Neighbor Joining:w
argchoice:FITCH, Fitch-Margoliash:F
argchoice:FITCH, Minimum Evolution:f
argchoice:KITSCH, Fitch-Margoliash constant evolutionary clock:K
argchoice:KITSCH, Minimum Evolution constant evolutionary clock:k
argchoice:Neighbor Joining:N
argchoice:UPGMA:U
argvalue:0

arg:POWER
arglabel:POWER (FITCH,KITCH only)
argtype:text
argtext:2.0

arg:NEGBRANCH
arglabel:ALLOW NEGATIVE BRANCH LENGTHS? (FITCH,KITCH only)
argtype:chooser
argchoice:Yes:y
argchoice:No:n
argvalue:1

arg:OUTGRP
arglabel:SEQUENCE # OF OUTGROUP:
argtype:slider
argmin:1
argmax:1000
argvalue:1

arg:SUBREP
arglabel:DO SUBREPLICATES?
argtype:chooser
argchoice:Yes:y
argchoice:No:n
argvalue:0

arg:GLOBAL
arglabel:DO GLOBAL REARRANGEMENTS?  (FITCH,KITCH only)
argtype:chooser
argchoice:Yes:y
argchoice:No:n
argvalue:0

arg:JUMBLE
argtype:chooser
arglabel:JUMBLE THE SEQUENCE ORDER?
argchoice:Yes:J
argchoice:No:n
argvalue:0   

arg:JSEED
argtype:slider
arglabel:_____Jumble random number seed
argmin:5
argmax:65535
argvalue:12345

arg:NUMJUM
argtype:slider
arglabel:_____Number of times to jumble
argmin:1
argmax:50
argvalue:1

arg:TERMOUT
argtype:chooser
arglabel:SHOW PROGRESS REPORT
argchoice:none:/dev/null
argchoice:on screen:/dev/tty
argchoice:to .log file:../../$OUTNAME.log
argvalue:0

arg:PRINTDATA
argtype:chooser
arglabel:PRINT SEQUENCE DATA TO OUTFILE?
argchoice:Yes:y
argchoice:No:n
argvalue:1   

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Tree editor:gde.treeoutput.csh -e in1.outtree in1.outfile $OUTNAME
argchoice:Drawing program:gde.treeoutput.csh -d in1.outtree in1.outfile $OUTNAME
argchoice:Output files:gde.treeoutput.csh -f in1.outtree in1.outfile $OUTNAME
argvalue:0

#arg:WHERE
#arglabel:WHERE TO SEND OUTPUT
#argtype:chooser
#argchoice:ATV: ($GDE_TEXTEDIT in1.outfile; rm in1.outfile)& (atv in1.outtree)& ($GDE_TEXTEDIT in1.outtree; rm in1.outtree)&  
#argchoice:Drawtree:($GDE_TEXTEDIT in1.outfile; rm in1.outfile)&  (drawtree.csh in1.outtree yes f 0 360 IE 360 reg $DAT/Phylip/font1 0.333 l in1.plotfile; $GDE_PSVIEW in1.plotfile; rm in1.plotfile)& ($GDE_TEXTEDIT in1.outtree; rm in1.outtree) &
#argchoice:Output files:mv in1.outfile $OUTNAME.outfile; mv in1.outtree $OUTNAME.treefile
#argvalue:0
 
arg:OUTNAME
arglabel:_____raw filename (no extension)
argtype:text
argtext:dnadist

in:in1
informat:genbank