# ---------------------- Phylip help ---------------------------------------
item:Phylip help
itemmethod:(netscape $GDE_HELP_DIR/$FILE)&

arg:FILE
argtype:choice_list
arglabel:Which program?
argchoice:clique:clique.html
argchoice:consense:consense.html
argchoice:contchar:contchar.html
argchoice:contml:contml.html
argchoice:contrast:contrast.html
argchoice:discrete:discrete.html
argchoice:distance:distance.html
argchoice:dnaboot:dnaboot.html
argchoice:dnacomp:dnacomp.html
argchoice:dnadist:dnadist.html
argchoice:dnainvar:dnainvar.html
argchoice:dnaml:dnaml.html
argchoice:dnamlk:dnamlk.html
argchoice:dnamove:dnamove.html
argchoice:dnapars:dnapars.html
argchoice:dnapenny:dnapenny.html
argchoice:dollop:dollop.html
argchoice:dolmove:dolmove.html
argchoice:dolpenny:dolpenny.html
argchoice:draw:draw.html
argchoice:drawgram:drawgram.html
argchoice:drawtree:drawtree.html
argchoice:factor:factor.html
argchoice:fitch:fitch.html
argchoice:gendist:gendist.html
argchoice:kitsch:kitsch.html
argchoice:main:main.html
argchoice:mix:mix.html
argchoice:move:move.html
argchoice:neighbor:neighbor.html
argchoice:penny:penny.html
argchoice:protpars:protpars.html
argchoice:read.me.general:read.me.general.html
argchoice:restml:restml.html
argchoice:seqboot:seqboot.html
argchoice:sequence:sequence.html


# ---------------------- Phylip 3.5 ---------------------------------------
item:Phylip 3.5
itemmethod:(rm -f outfile ; readseq -a -f12 in1 | sed "s/ YF//1" > infile;$PREEDIT  /usr/bin/X11/xterm -e  $PROGRAM;gedit outfile; treetool outtree; rm in1 )&
 
arg:PROGRAM
argtype:choice_list
arglabel:Which program to run?
argchoice:DNAPARS:dnapars
argchoice:DNABOOT:dnaboot
argchoice:DNAPENNY:dnapenny
argchoice:DNAML:dnaml
argchoice:DNAMLK:dnamlk
argchoice:DNACOMP:dnacomp
argchoice:DNAMOVE:dnamove
argchoice:DNAINVAR:dnainvar
argchoice:PROTPARS:protpars

arg:PREEDIT
argtype:chooser
arglabel:Edit input before running?
argchoice:No:
argchoice:Yes:gedit infile;
 
in:in1
informat:genbank
inmask:
insave:


# ------------------- Phylip 3.5 DNA Distance methods -------------------------
item:Phylip DNA Distance methods 
itemmethod:(readseq -a -f12 in1 | sed "s/ YF//1" > infile ;$PROG mv -f outfile infile; /usr/bin/X11/xterm -e dnadist;mv -f outfile infile; cp infile $DNA;  /usr/bin/X11/xterm -e neighbor; cp outtree intree; cp outfile $NEI; $PROGRAM  gedit outfile; cp outtree $TREE; treetool outtree;  /bin/rm -f in1 infile outfile intree outtree)&
 
arg:EXPLAIN
argtype:text
arglabel:To produce a bootstraped tree choose DNADIST+NEIGHOR+CONSENSE


arg:PROGRAM
arglabel:Which method?
argtype:chooser
argchoice:DNADIST+NEIGHBOR:
argchoice:DNADIST+NEIGHOR+CONSENSE: /usr/bin/X11/xterm -e  consense;

arg:PROG
arglabel:Run ?
argtype:chooser
argchoice:Run without Bootstrap:
argchoice:Run with Bootstrap: /usr/bin/X11/xterm -e  seqboot;

arg:DNA
argtype:text
arglabel:Name of DNADIST outfile?

arg:NEI
argtype:text
arglabel:Name of NEIGHBOR outfile?

arg:TREE
argtype:text
arglabel:Name of TREEFILE ?

arg:PREEDIT
argtype:chooser
arglabel:Edit input before running?
argchoice:No:
argchoice:Yes:gedit infile;
 
in:in1
informat:genbank
inmask:
insave:

# ------------------ Phylip 3.5  Protein Distance Methods --------------------
item:Phylip PROTEIN Distance methods 
itemmethod:(readseq -a -f12 in1 > infile ;$PROG mv -f outfile infile;  /usr/bin/X11/xterm -e protdist;mv -f outfile infile;  /usr/bin/X11/xterm -e neighbor; cp outtree intree; $PROGRAM  gedit outfile;treetool outtree;/bin/rm -f in1 infile outfile)&
 
arg:PROGRAM
arglabel:Which method?
argtype:chooser
argchoice:PROTDIST+NEIGHBOR:
argchoice:PROTDIST+NEIGHOR+CONSENSE: /usr/bin/X11/xterm -e  consense;

arg:PROG
arglabel:Which method?
argtype:chooser
argchoice:Bootstrap: /usr/bin/X11/xterm -e  seqboot;
argchoice:No Bootstrap:

arg:PREEDIT
argtype:chooser
arglabel:Edit input before running?
argchoice:No:
argchoice:Yes:gedit  infile;
 
in:in1
informat:genbank
inmask:
insave: