./bldna/PCD.old/Database/BLASTNlocal.blmenu.bak:239:                "Web Browser" "python $birch/script/blblastout.py --archive %in1%.blastn.asn1  --destination browser --outfmt %VOPTIONS%;"
./bldna/PCD.old/Database/BLASTNlocal.blmenu.bak:240:                "Text Editor" "python $birch/script/blblastout.py --archive  %in1%.blastn.asn1   --destination textedit --outfmt %VOPTIONS%;"
./bldna/PCD.old/Database/BLASTNlocal.blmenu.bak:241:                "HTML file" "python $birch/script/blblastout.py --archive  %in1%.blastn.asn1  --destination htmlfile --outfmt %VOPTIONS% --outfile %OUTNAME%;"
./bldna/PCD.old/Database/BLASTNlocal.blmenu.bak:242:                "Text file" "python $birch/script/blblastout.py --archive  %in1%.blastn.asn1  --destination textfile --outfmt %VOPTIONS% --outfile %OUTNAME%;"
./bldna/PCD.old/Database/BLASTNlocal.blmenu.bak:250:                "blnfetch" "python $birch/script/blblastout.py --archive  %in1%.blastn.asn1 --destination blnfetch --outfmt 7,sacc,stitle,sscinames,staxids,evalue,length,sframe,sstrand,slen,mismatch,gapopen,qstart,qend,sstart,send,bitscore,pident;"
./bldna/PCD.old/Database/BLASTNlocal.blmenu.bak:251:                "tsvfile"  "python $birch/script/blblastout.py --archive  %in1%.blastn.asn1 --destination tsvfile --outfmt 7,sacc,stitle,sscinames,staxids,evalue,length,sframe,sstrand,slen,mismatch,gapopen,qstart,qend,sstart,send,bitscore,pident --outfile %OUTNAME%;"
./bldna/PCD.old/Database/BLASTNlocal.blmenu.bak:259:                "BlastViewer" "python $birch/script/blblastout.py --archive %in1%.blastn.asn1 --destination blastviewer --outfmt 5;"
./bldna/PCD.old/Database/BLASTNlocal.blmenu.bak:260:                "xmlfile"  "python $birch/script/blblastout.py --archive %in1%.blastn.asn1 --destination xmlfile --outfmt 5 --outfile %OUTNAME%;"
./bldna/PCD.old/Database/BLASTXlocal.blmenu.template:236:                "Web Browser" "python $birch/script/blblastout.py --archive %in1%.blastx.asn1  --destination browser  --outfmt %VOPTIONS%;"
./bldna/PCD.old/Database/BLASTXlocal.blmenu.template:237:                "Text Editor" "python $birch/script/blblastout.py --archive %in1%.blastx.asn1   --destination textedit --outfmt %VOPTIONS%;"
./bldna/PCD.old/Database/BLASTXlocal.blmenu.template:238:                "HTML file" "python $birch/script/blblastout.py --archive %in1%.blastx.asn1  --destination htmlfile --outfmt %VOPTIONS% --outfile %OUTNAME%;"
./bldna/PCD.old/Database/BLASTXlocal.blmenu.template:239:                "Text file" "python $birch/script/blblastout.py --archive %in1%.blastx.asn1  --destination textfile --outfmt %VOPTIONS% --outfile %OUTNAME%;"
./bldna/PCD.old/Database/BLASTXlocal.blmenu.template:247:                "blpfetch" "python $birch/script/blblastout.py --archive %in1%.blastx.asn1 --destination blpfetch --outfmt 7,sacc,stitle,sscinames,staxids,evalue,length,slen,mismatch,gapopen,qstart,qend,sstart,send,bitscore,pident;"
./bldna/PCD.old/Database/BLASTXlocal.blmenu.template:248:                "tsvfile"  "python $birch/script/blblastout.py --archive %in1%.blastx.asn1 --destination tsvfile --outfmt 7,sacc,stitle,sscinames,staxids,evalue,length,slen,mismatch,gapopen,qstart,qend,sstart,send,bitscore,pident --outfile %OUTNAME%;"
./bldna/PCD.old/Database/BLASTXlocal.blmenu.template:257:                "BlastViewer" "python $birch/script/blblastout.py --archive %in1%.blastx.asn1 --destination blastviewer --outfmt 5;"
./bldna/PCD.old/Database/BLASTXlocal.blmenu.template:258:                "xmlfile"  "python $birch/script/blblastout.py --archive %in1%.blastx.asn1 --destination xmlfile --outfmt 5 --outfile %OUTNAME%;"
./bldna/PCD.old/Database/FASTXY.blmenu:167:#        shell       "(sed ""s/[#%]/>/""<%in1% >%in1%.fasta;nice -n 0 %PROGRAM% -T -Q -d %NUMOFALN% %MARKX% %MATRIX% %ZED% -E %EVALUE% %in1%.fasta %DBASE% %KTUP% > %in1%.out; python $birch/script/dbsout.py %in1%.out %WHERE%; rm %in1%*)&"
./bldna/PCD.old/Database/FASTXY.blmenu.template:162:#        shell       "(sed ""s/[#%]/>/""<%in1% >%in1%.fasta;nice -n 0 %PROGRAM% -T -Q -d %NUMOFALN% %MARKX% %MATRIX% %ZED% -E %EVALUE% %in1%.fasta %DBASE% %KTUP% > %in1%.out; python $birch/script/dbsout.py %in1%.out %WHERE%; rm %in1%*)&"
./bldna/PCD.old/Database/TBLASTXlocal.blmenu.template:231:                "Web Browser" "python $birch/script/blblastout.py --archive %in1%.tblastx.asn1  --destination browser --outfmt %VOPTIONS%;"
./bldna/PCD.old/Database/TBLASTXlocal.blmenu.template:232:                "Text Editor" "python $birch/script/blblastout.py --archive  %in1%.tblastx.asn1   --destination textedit --outfmt %VOPTIONS%;"
./bldna/PCD.old/Database/TBLASTXlocal.blmenu.template:233:                "HTML file" "python $birch/script/blblastout.py --archive  %in1%.tblastx.asn1  --destination htmlfile --outfmt %VOPTIONS% --outfile %OUTNAME%;"
./bldna/PCD.old/Database/TBLASTXlocal.blmenu.template:234:                "Text file" "python $birch/script/blblastout.py --archive  %in1%.tblastx.asn1  --destination textfile --outfmt %VOPTIONS% --outfile %OUTNAME%;"
./bldna/PCD.old/Database/TBLASTXlocal.blmenu.template:242:                "blnfetch" "python $birch/script/blblastout.py --archive  %in1%.tblastx.asn1 --destination blnfetch --outfmt 7,sacc,stitle,sscinames,staxids,evalue,length,sframe,sstrand,slen,mismatch,gapopen,qstart,qend,sstart,send,bitscore,pident;"
./bldna/PCD.old/Database/TBLASTXlocal.blmenu.template:243:                "tsvfile"  "python $birch/script/blblastout.py --archive  %in1%.tblastx.asn1 --destination tsvfile --outfmt 7,sacc,stitle,sscinames,staxids,evalue,length,sframe,sstrand,slen,mismatch,gapopen,qstart,qend,sstart,send,bitscore,pident --outfile %OUTNAME%;"
./bldna/PCD.old/Database/TBLASTXlocal.blmenu.template:251:                "BlastViewer" "python $birch/script/blblastout.py --archive %in1%.tblastx.asn1 --destination blastviewer --outfmt 5;"
./bldna/PCD.old/Database/TBLASTXlocal.blmenu.template:252:                "xmlfile"  "python $birch/script/blblastout.py --archive %in1%.tblastx.asn1 --destination xmlfile --outfmt 5 --outfile %OUTNAME%;"
./bldna/PCD/DNARNA/TACGrest.blmenu~:153:        shell       "(readseq -fgb -o=%in1%.tmp %in1%; python $BIRCH/script/tacg.py %TOPOLOGY% %ORDER% -n %MINSITE% %OVERHANG% -m %MINCUTS% -M %MAXCUTS% %REFILE% -w %WIDTH% %CUTS% %FRAGS% %LAMAP% %LIMAP% -g %MINFRAG%,%MAXFRAG% %TRANS% %STRANDS% -H --pdf %ADDITIONAL% %in1%.tmp %in1%.html %in1%.pdf; $RM_CMD %in1% %in1%.tmp; (chooseviewer.py file://$PWD/%in1%.html)& if [ -f %in1%.pdf ]; then ($BL_PDFViewer %in1%.pdf; $RM_CMD %in1%.pdf %in1%.html)& fi)&"
./bldna/PCD/Database/FASTXY.blmenu:160:#        shell       "(sed ""s/[#%]/>/""<%in1% >%in1%.fasta;nice -n 0 %PROGRAM% -T -Q -d %NUMOFALN% %MARKX% %MATRIX% %ZED% -E %EVALUE% %in1%.fasta %DBASE% %KTUP% > %in1%.out; python $birch/script/dbsout.py %in1%.out %WHERE%; rm %in1%*)&"
./bldna/PCD/Database/BLASTN.blmenu~:215:        shell       "(nice -n 4 blastn -remote -query %in1% -db %DBASE% -task %SEARCHTASK% -evalue %EVALUE% %STRAND% %DUST% %SMASK% %LMASK% %OQUERY% %EQUERY% %MATCHSCORES% -word_size %WORD% -outfmt %VOPTIONS% -max_target_seqs %MAXDISP% -show_gis -parse_deflines > %in1%.blastn; rm %in1%; python $BIRCH/script/blast2gi.py %in1%.blastn%in1%.tmpcsv; cat %in1%.tmpcsv | tr ',' '	' > %in1%.csv; rm %in1%.tmpcsv; %WHERE% ) &"
./bldna/PCD/Database/BLASTX.blmenu~:224:        shell       "(nice -n 4 blastx -remote -query %in1% -db %DBASE% -query_gencode %GENCODE% -evalue %EVALUE% %STRAND% %SEG% %SMASK% %LMASK% %OQUERY% %EQUERY% -matrix %MATRIX% %WORD% %GAPPED% -outfmt %VOPTIONS% -max_target_seqs %MAXDISP% -show_gis -parse_deflines > %in1%.blastx; python $BIRCH/script/blast2gi.py %in1%.blastx %in1%.tmpcsv; cat %in1%.tmpcsv | tr ',' '	' > %in1%.csv; rm %in1%.tmpcsv; %WHERE%) &"
./bldna/PCD/Database/TBLASTX.blmenu~:225:        shell       "(nice -n 10 tblastx -remote -query %in1% -db %DBASE% -query_gencode %GENCODE% -evalue %EVALUE% %STRAND% %SEG% %SMASK% %LMASK% %OQUERY% %EQUERY% -matrix %MATRIX% %WORD% -outfmt %VOPTIONS% -max_target_seqs %MAXDISP% > %in1%.tblastx; python $BIRCH/script/dbsout.py %in1%.tblastx %WHERE%; rm %in1%*) &"
./bldna/PCD/Edit/ExtractSubset.blmenu:43:        shell       "(%NAMES%; python $BIRCH/script/BLExtractSubset.py %in1%.nam %in1% %in1%.out; rm %in1%.nam %in1% ; %WHERE%)"
./bldna/PCD/Edit/ExtractSubset.blmenu.bak1:40:        shell       "(%NAMES%; python $BIRCH/script/BLExtractSubset.py %in1%.nam %in1% %in1%.out; rm %in1%.nam %in1% ; %WHERE%) &"
./bldna/PCD/File/ImportFree.blmenu:15:        shell       "python $BIRCH/script/free2fasta.py %INPUTFILE% %out1%;"
./bldna/PCD/Patterns/TACGpat.blmenu~:131:        shell       "(readseq -fgb -o=%in1%.tmp %in1%; python $BIRCH/script/tacg.py %TOPOLOGY% %DEGENERACY% %MATFILE% %PTRNSW% -w %WIDTH% %CUTS% %LAMAP% %LIMAP% %TRANS% %STRANDS% -H --pdf  %in1%.tmp %in1%.html %in1%.pdf; $RM_CMD %in1% %in1%.tmp; (chooseviewer.py file://$PWD/%in1%.html)&  if [ -f %in1%.pdf ]; then ($BL_PDFViewer %in1%.pdf; $RM_CMD %in1%.pdf %in1%.html)& fi)&"
./blmarker/PCD/File/ExportPhylDisc.blmenu:16:        shell       "python $BIRCH/script/phylcnv.py -inf tsv -outf pint %in1% %OUTPUTFILE%; $RM_CMD %in1%"
./blmarker/PCD/File/ImportPhylDisc.blmenu:22:        shell       "python $BIRCH/script/phylcnv.py -inf %FILETYPE% -outf tsv %INPUTFILE% %out1%"
./blmarker/PCD/File/SaveSel.blmenu:9:        "Phylip discrete data" "python $BIRCH/script/phylcnv.py -inf tsv -outf pint %in2% %OUTNAME%"
./blmarker/PCD/Phylogeny/DiscDist.blmenu:116:        "Tree editor" "python $BIRCH/script/bltreeoutput.py -e %in1%.outtree %in1%.outfile %OUTNAME%"
./blmarker/PCD/Phylogeny/DiscDist.blmenu:131:        #shell       "python $BIRCH/script/phylcnv.py -inf csv -outf pint %in1% %in1%.tmp; rm %in1%; ($birch/script/restdist.py %in1%.tmp %MODEL% %TRANSRATIO% %SITELEN% %METHOD% %REPLICATES% %PERCENT% %TCONMETH% %POWER% %GLOBAL% %NEGBRANCH% %OUTGRP% %JUMBLE% %NUMJUM% %TERMOUT% %PRINTDATA%  %in1%.outfile %in1%.outtree; rm %in1%.tmp; %WHERE%) &"
./blmarker/PCD/Phylogeny/DiscDist.blmenu:132:        shell       "python $BIRCH/script/phylcnv.py -inf csv -outf pint %in1% %in1%.tmp; rm %in1%; ($birch/script/restdist.py %in1%.tmp %MODEL% %TRANSRATIO% %SITELEN% %METHOD% %REPLICATES% %PERCENT% %TCONMETH% %POWER% %GLOBAL% %NEGBRANCH% %OUTGRP% %JUMBLE% %NUMJUM% %TERMOUT% %PRINTDATA%  %in1%.outfile %in1%.outtree; rm %in1%.tmp; %WHERE%)"
./blmarker/PCD/Phylogeny/DiscDist.blmenu.bak:116:        "Tree editor" "python $BIRCH/script/bltreeoutput.py -e %in1%.outtree %in1%.outfile %OUTNAME%"
./blmarker/PCD/Phylogeny/DiscDist.blmenu.bak:131:        shell       "python $BIRCH/script/phylcnv.py -inf csv -outf pint %in1% %in1%.tmp; rm %in1%; ($birch/script/restdist.py %in1%.tmp %MODEL% %TRANSRATIO% %SITELEN% %METHOD% %REPLICATES% %PERCENT% %TCONMETH% %POWER% %GLOBAL% %NEGBRANCH% %OUTGRP% %JUMBLE% %NUMJUM% %TERMOUT% %PRINTDATA%  %in1%.outfile %in1%.outtree; rm %in1%.tmp; %WHERE%) &"
./blmarker/PCD/Phylogeny/DiscPars.blmenu:116:        #shell       "python $BIRCH/script/phylcnv.py -inf tsv -outf pint %in1% %in1%.tmp; rm %in1%; (discpars.py %in1%.tmp %UTREE% %METHOD% %REPLICATES% %PERCENT% %TCONMETH% %PARSTYPE% %THRESHOLD% %OUTGRP% %JUMBLE% %NUMJUM% %TERMOUT% %ALLTREES%  %in1%.outfile %in1%.outtree %in1%.outtree.alltrees; $RM_CMD -f %in1%.tmp; %WHERE%) &"
./blmarker/PCD/Phylogeny/DiscPars.blmenu:117:        shell       "python $BIRCH/script/phylcnv.py -inf tsv -outf pint %in1% %in1%.tmp; rm %in1%; discpars.py %in1%.tmp %UTREE% %METHOD% %REPLICATES% %PERCENT% %TCONMETH% %PARSTYPE% %THRESHOLD% %OUTGRP% %JUMBLE% %NUMJUM% %TERMOUT% %ALLTREES%  %in1%.outfile %in1%.outtree %in1%.outtree.alltrees; $RM_CMD -f %in1%.tmp; %WHERE%"
./blmarker/PCD/Phylogeny/RESTML.blmenu:124:        #shell       "python $BIRCH/script/phylcnv.py -inf tsv -outf pint %in1% %in1%.tmp; rm %in1%; (restml.py %in1%.tmp %UTREE% %METHOD% %REPLICATES% %PERCENT% %ALLSITES% %SPEEDY% %GLOBAL% %SITENUM% %SITELEN% %OUTGRP% %JUMBLE% %NUMJUM% %TERMOUT% %PRINTDATA%  %in1%.outfile %in1%.outtree; rm %in1%.tmp; %WHERE%) &"
./blmarker/PCD/Phylogeny/RESTML.blmenu:125:        shell       "python $BIRCH/script/phylcnv.py -inf tsv -outf pint %in1% %in1%.tmp; rm %in1%; restml.py %in1%.tmp %UTREE% %METHOD% %REPLICATES% %PERCENT% %ALLSITES% %SPEEDY% %GLOBAL% %SITENUM% %SITELEN% %OUTGRP% %JUMBLE% %NUMJUM% %TERMOUT% %PRINTDATA%  %in1%.outfile %in1%.outtree; rm %in1%.tmp; %WHERE%"
./blnalign/PCD/Edit/ExtractSubset.blmenu:40:        shell       "(%NAMES%; python $BIRCH/script/BLExtractSubset.py %in1%.nam %in1% %in1%.out; rm %in1%.nam %in1% ; %WHERE%) &"
./blnalign/PCD/Patterns/TACGpat.blmenu~:131:        shell       "(readseq -fgb -o=%in1%.tmp %in1%; python $BIRCH/script/tacg.py %TOPOLOGY% %DEGENERACY% %MATFILE% %PTRNSW% -w %WIDTH% %CUTS% %LAMAP% %LIMAP% %TRANS% %STRANDS% -H --pdf  %in1%.tmp %in1%.html %in1%.pdf; $RM_CMD %in1% %in1%.tmp; (chooseviewer.py file://$PWD/%in1%.html)&  if [ -f %in1%.pdf ]; then ($BL_PDFViewer %in1%.pdf; $RM_CMD %in1%.pdf %in1%.html)& fi)&"
./blncbi/PCD/Edit/BLSORT.blmenu.current:265:        shell       "(python $BIRCH/script/blsort.py %in1% %in1%.tsv %S1%%S2%%S3%%S4% %DESCENDING%; blncbi %in1%.tsv; rm %in1%.*)&"
./blncbi/PCD/Edit/BLSORT.blmenu.current:271:        shell       "python $BIRCH/script/blsort.py %in2% %in2%.tsv %S1%%S2%%S3%%S4% %DESCENDING%;  mv %in2%.tsv %out2%"
./blnfetch/PCD/Edit/BLSORT.blmenu:265:        shell       "python $BIRCH/script/blsort.py %in1% %in1%.tsv %S1%%S2%%S3%%S4% %DESCENDING%; blnfetch %in1%.tsv; rm %in1%.*"
./blnfetch/PCD/Edit/BLSORT.blmenu:271:        shell       "python $BIRCH/script/blsort.py %in2% %in2%.tsv %S1%%S2%%S3%%S4% %DESCENDING%;  mv %in2%.tsv %out2%"
./blpalign/PCD/Edit/ExtractSubset.blmenu:40:        shell       "(%NAMES%; python $BIRCH/script/BLExtractSubset.py %in1%.nam %in1% %in1%.out; rm %in1%.nam %in1% ; %WHERE%) &"
./blpalign/PCD/Phylogeny/PROTDIST.blmenu:172:        shell       "cat %in1% | sed ""s/[\:\_]CDS/_/"" > %in1%.infile; rm %in1%; python $birch/script/protdist.py %in1%.infile %DMETHOD% %TRANSRATIO% %GC% %CATEGORIZATION% %METHOD% %REPLICATES% %BLOCKSIZE% %PERCENT% %TCONMETH% %POWER% %SUBREP% %GLOBAL% %NEGBRANCH% %OUTGRP% %JUMBLE% %NUMJUM% %TERMOUT% %ALLTREES% %PRINTDATA% %in1%.outfile %in1%.outtree %in1%.outtree.alltrees; rm %in1%.infile; %WHERE% "
./blpalign/PCD/Phylogeny/PROTDIST.blmenu~:158:        shell       "tr ""~"" ""-"" < %in1% | sed ""s/[\:\_]CDS/_/"" | readseq -a -f12 -pipe | sed ""s/ YF//1"" > %in1%.tmp; rm %in1%; (python $birch/script/protdist.py %in1%.tmp %DMETHOD% %TRANSRATIO% %GC% %CATEGORIZATION% %METHOD% %REPLICATES% %BLOCKSIZE% %PERCENT% %TCONMETH% %POWER% %SUBREP% %GLOBAL% %NEGBRANCH% %OUTGRP% %JUMBLE% %NUMJUM% %TERMOUT% %PRINTDATA% %in1%.outfile %in1%.outtree; rm %in1%.tmp; %WHERE%) &"
./blpalign/PCD/Phylogeny/PROTDIST.blmenu.bak1:158:        #shell       "tr ""~"" ""-"" < %in1% | sed ""s/[\:\_]CDS/_/"" | readseq -a -f12 -pipe | sed ""s/ YF//1"" > %in1%.tmp; rm %in1%; (python $birch/script/protdist.py %in1%.tmp %DMETHOD% %TRANSRATIO% %GC% %CATEGORIZATION% %METHOD% %REPLICATES% %BLOCKSIZE% %PERCENT% %TCONMETH% %POWER% %SUBREP% %GLOBAL% %NEGBRANCH% %OUTGRP% %JUMBLE% %NUMJUM% %TERMOUT% %PRINTDATA% %in1%.outfile %in1%.outtree; rm %in1%.tmp; %WHERE%)& "
./blpalign/PCD/Phylogeny/PROTDIST.blmenu.bak1:159:        shell       "tr ""~"" ""-"" < %in1% | sed ""s/[\:\_]CDS/_/"" | readseq -a -f12 -pipe > %in1%.tmp; rm %in1%; (python $birch/script/protdist.py %in1%.tmp %DMETHOD% %TRANSRATIO% %GC% %CATEGORIZATION% %METHOD% %REPLICATES% %BLOCKSIZE% %PERCENT% %TCONMETH% %POWER% %SUBREP% %GLOBAL% %NEGBRANCH% %OUTGRP% %JUMBLE% %NUMJUM% %TERMOUT% %PRINTDATA% %in1%.outfile %in1%.outtree; rm %in1%.tmp; %WHERE%) "
./blpalign/PCD/Phylogeny/PROTDIST.blmenu.bak2:163:        shell       "cat %in1% | sed ""s/[\:\_]CDS/_/"" > %in1%.infile; rm %in1%; python $birch/script/protdist.py %in1%.infile %DMETHOD% %TRANSRATIO% %GC% %CATEGORIZATION% %METHOD% %REPLICATES% %BLOCKSIZE% %PERCENT% %TCONMETH% %POWER% %SUBREP% %GLOBAL% %NEGBRANCH% %OUTGRP% %JUMBLE% %NUMJUM% %TERMOUT% %PRINTDATA% %in1%.outfile %in1%.outtree; rm %in1%.infile; %WHERE% "
./blpfetch/PCD/Edit/BLSORT.blmenu:265:        shell       "(python $BIRCH/script/blsort.py %in1% %in1%.tsv %S1%%S2%%S3%%S4% %DESCENDING%; blpfetch %in1%.tsv; rm %in1%.*)&"
./blpfetch/PCD/Edit/BLSORT.blmenu:271:        shell       "python $BIRCH/script/blsort.py %in2% %in2%.tsv %S1%%S2%%S3%%S4% %DESCENDING%;  mv %in2%.tsv %out2%"
./blprotein/PCD/Database/BLASTP.blmenu~:207:        shell       "(nice -n 4 blastp -remote -query %in1% -db %DBASE% -task %SEARCHTASK% -matrix %MATRIX% -evalue %EVALUE% %WORD% %SEG% %LMASK% %SMASK% %EQUERY% %OQUERY% %COMP% -outfmt %VOPTIONS% -max_target_seqs %MAXDISP% -out %in1%.blastp -show_gis -parse_deflines; python $BIRCH/script/blast2gi.py %in1%.blastp %in1%.tmpcsv | tr ',' '	' > %in1%.csv; rm %in1%.tmpcsv; %WHERE% ) &"
./blprotein/PCD/Database/TBLASTN.blmenu~:226:        shell       "(nice -n 4 tblastn -remote -query %in1% -db %DBASE% -db_gencode %GENCODE% -evalue %EVALUE% %SEG% %SMASK% %LMASK% %OQUERY% %EQUERY% -matrix %MATRIX% %WORD% %COMP% -outfmt %VOPTIONS% -max_target_seqs %MAXDISP% -show_gis -parse_deflines > %in1%.tblastn; python $BIRCH/script/blast2gi.py %in1%.tblastn %in1%.tmpcsv; cat %in1%.tmpcsv | tr ',' '	' > %in1%.csv; rm %in1%.tmpcsv; %WHERE% ) &"
./blprotein/PCD/Edit/ExtractSubset.blmenu:47:        shell       "(%NAMES%; python $BIRCH/script/BLExtractSubset.py %in1%.nam %in1% %in1%.out; rm %in1%.nam %in1% ; %WHERE%) &"
./blprotein/PCD/Edit/ExtractSubset.blmenu.bak1:40:        shell       "(%NAMES%; python $BIRCH/script/BLExtractSubset.py %in1%.nam %in1% %in1%.out; rm %in1%.nam %in1% ; %WHERE%) &"
./blprotein/PCD.old/Database/BLASTPlocal.blmenu.template:222:                "Web Browser" "python $birch/script/blblastout.py --archive %in1%.blastp.asn1  --destination browser --outfmt %VOPTIONS%;"
./blprotein/PCD.old/Database/BLASTPlocal.blmenu.template:223:                "Text Editor" "python $birch/script/blblastout.py --archive %in1%.blastp.asn1   --destination textedit --outfmt %VOPTIONS%;"
./blprotein/PCD.old/Database/BLASTPlocal.blmenu.template:224:                "HTML file" "python $birch/script/blblastout.py --archive %in1%.blastp.asn1  --destination htmlfile --outfmt %VOPTIONS% --outfile %OUTNAME%;"
./blprotein/PCD.old/Database/BLASTPlocal.blmenu.template:225:                "Text file" "python $birch/script/blblastout.py --archive %in1%.blastp.asn1  --destination textfile --outfmt %VOPTIONS% --outfile %OUTNAME%;"
./blprotein/PCD.old/Database/BLASTPlocal.blmenu.template:233:                "blpfetch" "python $birch/script/blblastout.py --archive %in1%.blastp.asn1 --destination blpfetch --outfmt 7,sacc,stitle,sscinames,staxids,evalue,length,slen,mismatch,gapopen,qstart,qend,sstart,send,bitscore,pident;"
./blprotein/PCD.old/Database/BLASTPlocal.blmenu.template:234:                "tsvfile"  "python $birch/script/blblastout.py --archive %in1%.blastp.asn1 --destination tsvfile --outfmt 7,sacc,stitle,sscinames,staxids,evalue,length,slen,mismatch,gapopen,qstart,qend,sstart,send,bitscore,pident --outfile %OUTNAME%;"
./blprotein/PCD.old/Database/BLASTPlocal.blmenu.template:242:                "BlastViewer" "python $birch/script/blblastout.py --archive %in1%.blastp.asn1 --destination blastviewer --outfmt 5;"
./blprotein/PCD.old/Database/BLASTPlocal.blmenu.template:243:                "xmlfile"  "python $birch/script/blblastout.py --archive %in1%.blastp.asn1 --destination xmlfile --outfmt 5 --outfile %OUTNAME%;"
./blprotein/PCD.old/Database/TBLASTNlocal.blmenu.template:232:                "Web Browser" "python $birch/script/blblastout.py --archive %in1%.tblastn.asn1  --destination browser --outfmt %VOPTIONS%;"
./blprotein/PCD.old/Database/TBLASTNlocal.blmenu.template:233:                "Text Editor" "python $birch/script/blblastout.py --archive %in1%.tblastn.asn1   --destination textedit --outfmt %VOPTIONS%;"
./blprotein/PCD.old/Database/TBLASTNlocal.blmenu.template:234:                "HTML file" "python $birch/script/blblastout.py --archive %in1%.tblastn.asn1  --destination htmlfile --outfmt %VOPTIONS% --outfile %OUTNAME%;"
./blprotein/PCD.old/Database/TBLASTNlocal.blmenu.template:235:                "Text file" "python $birch/script/blblastout.py --archive %in1%.tblastn.asn1  --destination textfile --outfmt %VOPTIONS% --outfile %OUTNAME%;"
./blprotein/PCD.old/Database/TBLASTNlocal.blmenu.template:243:                "blnfetch" "python $birch/script/blblastout.py --archive %in1%.tblastn.asn1 --destination blnfetch --outfmt 7,sacc,stitle,sscinames,staxids,evalue,length,sframe,sstrand,slen,mismatch,gapopen,qstart,qend,sstart,send,bitscore,pident;"
./blprotein/PCD.old/Database/TBLASTNlocal.blmenu.template:244:                "tsvfile"  "python $birch/script/blblastout.py --archive %in1%.tblastn.asn1 --destination tsvfile --outfmt 7,sacc,stitle,sscinames,staxids,evalue,length,sframe,sstrand,slen,mismatch,gapopen,qstart,qend,sstart,send,bitscore,pident --outfile %OUTNAME%;"
./blprotein/PCD.old/Database/TBLASTNlocal.blmenu.template:252:                "BlastViewer" "python $birch/script/blblastout.py --archive %in1%.tblastn.asn1 --destination blastviewer --outfmt 5;"
./blprotein/PCD.old/Database/TBLASTNlocal.blmenu.template:253:                "xmlfile"  "python $birch/script/blblastout.py --archive %in1%.tblastn.asn1 --destination xmlfile --outfmt 5 --outfile %OUTNAME%;"
./bltable/PCD/Edit/BLSORT.blmenu:265:        shell       "(python $BIRCH/script/blsort.py %in1% %in1%.tsv %S1%%S2%%S3%%S4% %DESCENDING%; bltable %in1%.tsv; rm %in1%.*)&"
./bltable/PCD/Edit/BLSORT.blmenu:271:        shell       "python $BIRCH/script/blsort.py %in2% %in2%.tsv %S1%%S2%%S3%%S4% %DESCENDING%;  mv %in2%.tsv %out2%"
./bltree/PCD/Draw/ATV.blmenu.old:12:        shell       "(python $BIRCH/script/flat2tree.py %in1% %in1%.treefile; rm %in1%; atv %in1%.treefile; rm %in1%.treefile)&"
./bltree/PCD/Draw/Drawtree.blmenu:113:        shell       "(flat2tree.py %in1% %in1%.treefile; rm %in1%; if test -s %in1%.treefile; then python $BIRCH/script/drawtree.py %in1%.treefile %USELEN% %LORIENT% %LANGLE% %ROTATION% %ITERATE% %ARCANGLE% %REGULARIZATION% $BIRCH/dat/Phylip/%FONTFILE% %CHARHEIGHT% %OUTFORMAT% %in1%.plotfile.ps; rm %in1%.treefile; %WHERE% fi)"
./bltree/PCD/Draw/Treetool.blmenu.old:6:exec        "(python $BIRCH/script/flat2tree.py %in1% %in1%.treefile; rm %in1%; treetool %in1%.treefile; rm %in1%.treefile) &"
./bltree/PCD/Evaluate/consensus.blmenu:53:        shell       "python $BIRCH/script/flat2tree.py %in1% %in1%.intree; rm %in1%; $birch/script/consense.py %in1%.intree %METHOD% %FRACTION% %OUTGROUP% %ROOTED% %in1%.outfile %in1%.outtree; rm %in1%.intree; %WHERE%"
./bltree/PCD/Evaluate/treedist.blmenu:54:        shell       "python $BIRCH/script/flat2tree.py %in1% %in1%.intree; rm %in1%; $BIRCH/script/treedist.py %in1%.intree %DISTTYPE% %ROOTED% %WHICHDIST% %OUTSTYLE% %in1%.outfile; rm %in1%.intree; %WHERE%"
./bltree/PCD/File/ExportTree.blmenu:16:        shell       "(python $BIRCH/script/flat2tree.py %in1% %OUTPUTFILE%; $RM_CMD %in1%)"
./bltree/PCD/File/ImportTree.blmenu:15:        shell       "python $birch/script/tree2flat.py %INPUTFILE% %out1%"
./bltree/PCD/File/SaveSel.blmenu:8:        "Phylip treefile" "python $BIRCH/script/flat2tree.py %in2% %Name%"
./obsolete/bldna.pcd/PCD/Database/BLASTN.blmenu:98:        shell       "(sed ""s/[#%]/>/""<%in1% >%in1%.fasta; nice -n 10 blastcl3 -i %in1%.fasta -p blastn -d %DBASE% %RESTRICT% -S %STRANDS% -g %GAPPED% -e %EVALUE% -m %VOPTIONS%  > %in1%.blastn; python $BIRCH/script/dbsout.py %in1%.blastn %WHERE%; rm %in1%*) &"
./obsolete/bldna.pcd/PCD/Database/BLASTX.blmenu:115:        shell       "(sed ""s/[#%]/>/""<%in1% >%in1%.fasta; nice -n 10 blastcl3 -i %in1%.fasta -p blastx -d %DBASE% %RESTRICT% -M %MATRIX% -Q %GENCODE%  -D %GENCODE% -g %GAPPED% -e %EVALUE% -m %VOPTIONS%  > %in1%.blastx; python $BIRCH/script/dbsout.py %in1%.blastx %WHERE%; rm %in1%*) &"
./obsolete/bldna.pcd/PCD/Database/FASTADNA.blmenu:98:        shell       "(sed ""s/[#%]/>/""<%in1% >%in1%.fasta; nice -n 10 %PROGRAM% -Q -n -b %NUMOFSCORES% -d %NUMOFALN%  %MARKX% %ZED% -E %EVALUE% %in1%.fasta %DBASE% %KTUP% > %in1%.out; python $birch/script/dbsout.py %in1%.out %WHERE%; rm %in1%*) &"
./obsolete/bldna.pcd/PCD/Database/FASTXY.blmenu:111:        shell       "(sed ""s/[#%]/>/""<%in1% >%in1%.fasta;nice -n 10 %PROGRAM% -Q -d %NUMOFALN% %MARKX% %MATRIX% %ZED% -E %EVALUE% %in1%.fasta %DBASE% %KTUP% > %in1%.out; python $birch/script/dbsout.py %in1%.out %WHERE%; rm %in1%*) &"
./obsolete/bldna.pcd/PCD/Database/TBLASTX.blmenu:90:        shell       "(sed ""s/[#%]/>/""<%in1% >%in1%.fasta; nice -n 10 blastcl3 -i %in1%.fasta -p tblastx -d %DBASE% %RESTRICT% -g %GAPPED% -e %EVALUE% -m %VOPTIONS%  > %in1%.tblastn; python $BIRCH/script/dbsout.py %in1%.tblastn %WHERE%; rm %in1%*) &"
./obsolete/bldna.pcd/PCD/Edit/ExtractSubset.blmenu:36:        shell       "(%NAMES%; python $BIRCH/script/BLExtractSubset.py %in1%.nam %in1% %in1%.out; rm %in1%.nam %in1% ; %WHERE%) &"
./obsolete/bltree.pcd/PCD/Draw/ATV.blmenu:11:        shell       "(python $BIRCH/script/flat2tree.py %in1% %in1%.treefile; rm %in1%; atv %in1%.treefile; rm %in1%.treefile)&"
./obsolete/bltree.pcd/PCD/Draw/Drawgram.blmenu:110:        shell       "(python $BIRCH/script/flat2tree.py %in1% %in1%.treefile; rm %in1%; if test -s %in1%.treefile; then (python $BIRCH/script/drawgram.py %in1%.treefile %TORIENT% %TSTYLE% %USELEN% %LANGLE% %DBRATIO% %LDRATIO% $BIRCH/dat/Phylip/%FONTFILE% %CHARHEIGHT% %ANCESTNODE% %OUTFORMAT% %in1%.plotfile; rm %in1%.treefile; %WHERE% ) & fi)"
./obsolete/bltree.pcd/PCD/Draw/Drawtree.blmenu:110:        shell       "(python $BIRCH/script/flat2tree.py %in1% %in1%.treefile; rm %in1%; if test -s %in1%.treefile; then python $BIRCH/script/drawtree.py %in1%.treefile %USELEN% %LORIENT% %LANGLE% %ROTATION% %ITERATE% %ARCANGLE% %REGULARIZATION% $BIRCH/dat/Phylip/%FONTFILE% %CHARHEIGHT% %OUTFORMAT% %in1%.plotfile; rm %in1%.treefile; %WHERE% fi)&"
./obsolete/bltree.pcd/PCD/Evaluate/consensus.blmenu:51:        shell       "(python $BIRCH/script/flat2tree.py %in1% %in1%.intree; rm %in1%; $birch/script/consense.py %in1%.intree %METHOD% %FRACTION% %OUTGROUP% %ROOTED% %in1%.outfile %in1%.outtree; rm %in1%.intree; %WHERE%)&"
./obsolete/bltree.pcd/PCD/Evaluate/treedist.blmenu:51:        shell       "(python $BIRCH/script/flat2tree.py %in1% %in1%.intree; rm %in1%; $BIRCH/script/treedist.py %in1%.intree %DISTTYPE% %ROOTED% %WHICHDIST% %OUTSTYLE% %in1%.outfile; rm %in1%.intree; %WHERE%)&"
./obsolete/bltree.pcd/PCD/File/ExportTree.blmenu:14:        shell       "(python $BIRCH/script/flat2tree.py %in1% %OUTPUTFILE%; $RM_CMD %in1%)"
./obsolete/bltree.pcd/PCD/File/ImportTree.blmenu:13:        shell       "python $birch/script/tree2flat.py %INPUTFILE% %out1%;"
./obsolete/bltree.pcd/PCD/File/SaveSel.blmenu:8:        "Phylip treefile" "python $BIRCH/script/flat2tree.py %in2% %Name%"