1c1
< #------------------------- DNAML ( 4/10/2006)  --------------------------
---
> #------------------------- DNAML ( 1/27/2005)  --------------------------
4,6c4,5
< itemmethod: tr "~" "-" < in1 | sed "s/[\:\_]CDS/_/" | readseq -a -f12 -pipe | sed "s/ YF//1" > in1.tmp; rm in1; (dnaml.csh in1.tmp $UTREE $UFN $PROGRAM $TRATIO $SPEEDY $GLOBAL $METHOD $BSEED $REPLICATES $BLOCKSIZE $PERCENT $JUMBLE $JSEED $NUMJUM $OUTGRP $TERMOUT $PRINTDATA in1.outfile in1.outtree; rm in1.tmp; $WHERE) &
< itemhelp:doc/Phylip/dnaml.html
< itemopen:gde_help_viewer.csh
---
> itemmethod: tr "~" "-" < in1 | sed "s/[\:\_]CDS/_/" | readseq -a -f12 -pipe | sed "s/ YF//1" > in1.tmp; rm in1; (dnaml.csh in1.tmp $UTREE $UFN $PROGRAM $TRATIO $SPEEDY $GLOBAL $METHOD $BSEED $REPLICATES $BLOCKSIZE $PERCENT $JUMBLE $JSEED $NUMJUM $OUTGRP $TERMOUT $PRINTDATA in1.outfile in1.treefile; rm in1.tmp; $WHERE) &
> itemhelp:doc/Phylip/dnaml.txt
132,134c131,133
< 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 $OUTNAME
---
> argchoice:ATV: ($GDE_TEXTEDIT in1.outfile; rm in1.outfile)& (atv in1.treefile)& ($GDE_TEXTEDIT in1.treefile; rm in1.treefile)&  
> argchoice:Drawtree:($GDE_TEXTEDIT in1.outfile; rm in1.outfile)&  (drawtree.csh in1.treefile 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.treefile; rm in1.treefile) &
> argchoice:Output files:mv in1.outfile $OUTNAME.outfile; mv in1.treefile $OUTNAME.treefile
136,143d134
< 
< #arg:WHERE
< #arglabel:WHERE TO SEND OUTPUT
< #argtype:chooser
< #argchoice:ATV: ($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
