; 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 [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 [version=11] ;[version=50] ; updates for release 0.5a, jan'96 ; !! NOTE: this [version=] flag DOESN'T REMOVE existing vars, just adds new or changes ; try w/ 'var=' empty declaration? [paths] ; can use UNIX standard path descriptions here. DCLAP converts to local OS ; e.g., /root/path/to/somewhere -- full path from a root disk ; or, relative/path/to/somewhere -- relative path from app folder ; okay to use local OS conventions, but avoid "/" in path if not UNIX 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... lsadt=DeSoete LSADTree... drawtree=Draw unrooted Tree... drawgram=Draw Cladogram... ;dnaml=Phylip DNAML... [drawgram] form=$apps:drawgram.html [drawtree] form=$apps:drawtree.html [lsadt] form=$apps:lsadt.html [clustal] form=$apps:clustalw.html desc path help cmd infile seqformat minseq outfile1 outfile2 [cap] form=$apps:cap2.html desc path help cmd infile seqformat minseq outfile1 [fastdnaml] form=$apps:fastdnaml.html desc path help cmd infile seqformat minseq outfile1 outfile2 outfile3 [dnaml] form=$apps:dnaml.html desc path help cmd infile stdin seqformat minseq outfile1 outfile2 ;desc=A DNA max likelihood phylogeny estimator, from Phylip ;path=$apps:dnaml ;help=$apps:dnaml.doc ;cmd= ;stdin=$temp:dnaml.inseq ;seqformat=phylip ;minseq=2 ;outfile1=$apps:treefile biotree/newick ;outfile2=$apps:outfile text/plain