; SeqPup.prefs 
; default preferences for application

[version=5]
; increase version # each time this is edited to get app to update
; prefs.  You can add a new [version=6] section at the end and
; any new values after that will replace version=5 values.

[general]
gOptionIsOn=1
gShortFolder=0

[paths]
temp=
tables=tables
apps=apps
help=help

[data]
codon=tables:codon.table
renzyme=tables:renzyme.table
color=tables:color.table

[menus]
menubar=file,edit,seq,inet,childapp,window
file=File,New/N,Open.../O,Close/W,-,Save/S,Save As...,-,Print,Help/H,Quit/Q
edit=Edit,Undo/U,-,Cut/X,Copy/C,Paste/V,Clear,-,Select All/A
seq=Sequence
inet=Internet
childapp=ChildApp
window=Windows

[apps]
clustal=ClustalW Multiple align...
cap=CAP Contig assembly...
fastdnaml=FastDNAml...
;dnaml=Phylip DNAML...

[clustal]
desc=A multiple sequence alignment application
path=$apps:clustalw
help=$apps:clustalw.doc
;cmd=/infile=$temp:clustal.inseq /outfile=$temp:clustal.outseq /output=gcg /align
cmd=/infile=clustal.inseq /outfile=clustal.outseq /output=gcg /align
infile=$apps:clustal.inseq
seqformat=nbrf
minseq=2
outfile1=$apps:clustal.outseq	biosequence/msf
outfile2=$apps:clustal.dnd	biotree/newick

[cap]
desc=A gel contig assembly application
path=$apps:cap2
help=$apps:cap2.doc
;cmd=$temp:cap.inseq $temp:cap.outseq 20 85
cmd=cap.inseq cap.outseq 20 85
infile=$apps:cap.inseq
seqformat=fasta
minseq=2
outfile1=$apps:cap.outseq	biosequence/fasta
dlog1=input name=minoverlap value="20" title="Min. number bases overlap"
dlog2=input name=pctmatch value="85" title="Percent match"

[fastdnaml]
desc=A faster DNA max likelihood phylogeny estimator
path=$apps:fastDNAml
help=$apps:fastDNAml.doc
cmd=
infile=$apps:infile
seqformat=phylip
minseq=2
outfile1=$apps:outfile	text/plain
outfile2=$apps:checkpoint.0	text/plain

[dnaml]
desc=A DNA max likelihood phylogeny estimator, from Phylip
path=$apps:dnaml
help=$apps:dnaml.doc
cmd=< $temp:dnaml.inseq
infile=$temp:dnaml.inseq
seqformat=phylip
minseq=2
outfile1=$apps:outfile	text/plain
outfile2=$apps:treefile	biotree/newick

[windows]
fgLockText=1
fgUseColor=1
fgWinRect=211 87 781 389
gRichDocRect=10 34 500 404

[fonts]
gNameFontName=Times
gNameFontSize=10
gNameStyle=0
gBaseFontName=Courier
gBaseFontSize=10
gBaseStyle=0
gIndexFontName=Times
gIndexFontSize=9
gIndexStyle=0
gSeqFontName=Courier
gSeqFontSize=10
gSeqStyle=2
gTextFontName=Courier
gTextFontSize=10

[seqprint]
gNameLeft=0
gNameRight=1
gIndexLeft=1
gIndexRight=1
gIndexTop=1
gColored=0
gShowComplement=1
gThreeLetAA=0
gShowAA1=1
gShowAA2=1
gShowAA3=1
gShowCompAA1=1
gShowCompAA2=1
gShowCompAA3=1
gOnlyORF=0
gBasesPerLine=60

[remap]
gShowAllZymes=1
gShowCutpoints=1
gShowNoncutters=1
gShowExcludedCutters=1
gREMinCuts=1
gREMaxCuts=999



[version=6]
; updates for release 0.4i, aug'95

[seqdoc]
gWriteMasks=1
gMinCommonPercent=70
fgStartDoc=1
fgViewMode=0