item:ProbCons itemmeta: P seqtype:* itemmethod:(GOTO_LOCAL_DIR; \ arb_sed 's/#/>HASH_/' PERCENT_/' | \ arb_sed 's/"/>QUOTE_/'| \ arb_sed 's/@/>AT_/' | \ arb_sed '/^[^>]/ y/./-/' > probcons_in; \ RUN_IN_WINDOW(($ARBHOME/bin/probcons -pre $PRE_TRAINING_REPS -ir $PASSES -c $REPS probcons_in > probcons_out;)); \ arb_sed 's/>HASH_/#/' PERCENT_/%/' | \ arb_sed 's/>QUOTE_/"/' | \ arb_sed 's/>AT_/@/' > TmpOutputFile; RM_LOCAL_FILES(probcons_in* probcons_out* TmpInputFile) ) arg:REPS argtype:choice_menu arglabel:Passes of consistency transformation argtype:slider argmin:0 argmax:5 argvalue:2 arg:PASSES arglabel:Passes of iterative refinement argtype:slider argmin:0 argmax:1000 argvalue:100 arg:PRE_TRAINING_REPS arglabel:Rounds of pre-training before aligning the sequences argtype:slider argmin:0 argmax:20 argvalue:0 in:TmpInputFile informat:flat intyped:detailed insave: out:TmpOutputFile outformat:flat outaligned:yes //---------------------------------------------------- item:Muscle itemmeta: M seqtype:* itemmethod:(GOTO_LOCAL_DIR; \ arb_sed 's/#/>HASH_/' PERCENT_/' | \ arb_sed 's/"/>QUOTE_/'| \ arb_sed 's/@/>AT_/' | \ arb_sed '/^[^>]/ y/./-/' > muscle_in; \ RUN_IN_WINDOW(($ARBHOME/bin/muscle $SCORE $DIAGS $ANCHORS $DIMER $BRENNER -in muscle_in -out muscle_out -maxiters $MAXITERS;)); \ arb_sed 's/>HASH_/#/' PERCENT_/%/' | \ arb_sed 's/>QUOTE_/"/' | \ arb_sed 's/>AT_/@/' > TmpOutputFile; RM_LOCAL_FILES(muscle_in* muscle_out* TmpInputFile)) arg:MAXITERS argtype:text arglabel:Maximum number of iterations to run\n(use 2 for large datasets) argtext:16 //arg:ANCHORS //argtype:choice_menu //arglabel:Use anchor optimization in tree dependent refinement iterations //argchoice:Yes(default):-anchors //argchoice:No:-noanchors //arg:BRENNER //argtype:choice_menu //arglabel:Use Steven Brenner's method for computing the root alignment //argchoice:No(default): //argchoice:Yes:-brenner //arg:DIMER //argtype:choice_menu //arglabel:Use dimer approximation for the SP score\n(faster, slightly less accurate) //argchoice:No(default): //argchoice:Yes:-dimer //arg:DIAGS //argtype:choice_menu //arglabel:Use diagonal optimizations\n(faster, especially for closely related sequences,\nbut may be less accurate) //argchoice:No(default): //argchoice:Yes:-diags //arg:SCORE //argtype:choice_menu //arglabel:Scoring //argchoice:Log-expectation profile score (VTML240)(default):-le //argchoice:Sum-of-pairs protein profile score (PAM200):-sp //argchoice:Sum-of-pairs profile score (VTML240):-sv in:TmpInputFile informat:flat intyped:detailed insave: out:TmpOutputFile outformat:flat outaligned:yes //------------------------------------------------------------------- item:Mafft itemmeta: f seqtype:* itemmethod:(GOTO_LOCAL_DIR; \ arb_sed 's/#/>HASH_/' PERCENT_/' | \ arb_sed 's/"/>QUOTE_/'| \ arb_sed 's/@/>AT_/' | \ arb_sed '/^[^>]/ y/./-/' > mafft_in; \ RUN_IN_WINDOW(($ARBHOME/bin/$COMMAND $METHOD --preservecase --ep $OFFSET $SCORING_MATRIX mafft_in > mafft_out;)); \ arb_sed 's/>HASH_/#/' PERCENT_/%/' | \ arb_sed 's/>QUOTE_/"/' | \ arb_sed 's/>AT_/@/' > TmpOutputFile; RM_LOCAL_FILES(mafft_in* TmpInputFile mafft_out*)) itemhelp:mafft.help arg:COMMAND argtype:choice_menu arglabel:Method argchoice:Auto:mafft --auto argchoice:L-INS-i:mafft-linsi argchoice:G-INS-i:mafft-ginsi argchoice:E-INS-i:mafft-einsi argchoice:Q-INS-i:mafft-qinsi argchoice:X-INS-i:mafft-xinsi argchoice:FFT-NS-i:mafft-fftnsi argchoice:FFT-NS-2:mafft-fftns argchoice:NW-NS-i:mafft-nwnsi argchoice:NW-NS-2:mafft-nwns arg:SCORING_MATRIX argtype:choice_menu arglabel:Scoring matrix argchoice:BLOSUM62:--bl 62 argchoice:BLOSUM30:--bl 30 argchoice:BLOSUM45:--bl 45 argchoice:BLOSUM80:--bl 80 argchoice:JTT100:--jtt 100 argchoice:JTT200:--jtt 200 argchoice:JTT200:--jtt 200 argchoice:1PAM / K=2:--kimura 1 argchoice:20PAM / K=2:--kimura 20 argchoice:200PAM / K=2:--kimura 200 arg:OFFSET argtype:slider argmin:0.0 argmax:1.0 arglabel:Offset value [0..1]\n(use values >0.1 for closely related sequences) argtext:0.5 in:TmpInputFile informat:flat intyped:detailed insave: out:TmpOutputFile outformat:flat outaligned:yes //-------------------------------------------------------- item:ClustalW automatic itemmeta: W seqtype:* itemmethod:(GOTO_LOCAL_DIR; \ tr '"%//' '>' clus_in; \ RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align ; \ cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >TmpOutputFile; )); \ RM_LOCAL_FILES(clus_in* TmpInputFile)) itemhelp:clustalw.help in:TmpInputFile informat:flat insave: out:TmpOutputFile outformat:flat outaligned:yes // -------------------------------------------------------------------------------- item:Create ClustalW Profile 2 itemmeta: C seqtype:* itemmethod:(GOTO_LOCAL_DIR ; tr '"%//' '>' ../clus_prf ; RM_LOCAL_FILES(TmpInputFile)) itemhelp:clustalw.help in:TmpInputFile informat:flat insave: // -------------------------------------------------------------------------------- item:ClustalW Profile Alignment itemmeta: A seqtype:* itemmethod:(GOTO_LOCAL_DIR; \ tr '"%//' '>' clus_in; \ RUN_IN_WINDOW((clustalw -output=PIR -profile1=clus_in -profile2=../clus_prf -align ; \ cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )); \ RM_LOCAL_FILES(clus_in* TmpInputFile)) itemhelp:clustalw.help in:TmpInputFile informat:flat insave: out:TmpOutputFile outformat:flat outaligned:yes // -------------------------------------------------------------------------------- item:ClustalW DNA Alignment (fast) seqtype: N itemmeta: N itemmethod:(GOTO_LOCAL_DIR; \ tr '"%//' '>' clus_in ; \ RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \ -quicktree $INTERACTIVE \ -ktuple=$KTUPLE -topdiags=$TOPDIAGS \ -window=$WINDOW -pairgap=$PAIRGAP \ -score=$SCORE \ -type=DNA -transweight=$TRANSWEIGHT \ -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \ -dnamatrix=$DNAMATRIX; \ cat clus_in.pir | arb_sed "s/^>DL;/#/g" | arb_sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \ RM_LOCAL_FILES(clus_in* TmpInputFile)) itemhelp:clustalw.help // parameters for fast pairwise alignment: arg:PAIRGAP arglabel:Gap penalty (pairwise ali) argtype:slider argmin:1 argmax:500 argvalue:5 arg:KTUPLE arglabel:K-tuple size argtype:slider argmin:1 argmax:4 argvalue:2 arg:TOPDIAGS arglabel:No. of top diagonals argtype:slider argmin:1 argmax:50 argvalue:4 arg:WINDOW arglabel:Window size argtype:slider argmin:1 argmax:50 argvalue:4 // parameters for multiple alignment: arg:DNAMATRIX argtype:choice_menu arglabel:Weighting matrix (multiple ali) argchoice:IUB:IUB argchoice:CLUSTALW:CLUSTALW arg:GOP argtype:slider arglabel:Gap Open Penalty argmin:0 argmax:100 argvalue:15 arg:GEP arglabel:Gap Extend Penalty argtype:slider argmin:0 argmax:10 argvalue:6.66 arg:MAXDIV arglabel:% identity for delay argtype:slider argmin:0 argmax:100 argvalue:30 arg:TRANSWEIGHT arglabel:Transition weight argtype:slider argmin:0.0 argmax:1.0 argvalue:0.5 arg:INTERACTIVE arglabel:Interactive argtype:choice_menu argchoice:No: argchoice:Yes:-interactive in:TmpInputFile informat:flat insave: out:TmpOutputFile outformat:flat outaligned:yes // -------------------------------------------------------------------------------- item:ClustalW DNA Alignment (slow & accurate) seqtype: N itemmeta: s itemmethod:(GOTO_LOCAL_DIR; \ tr '"%//' '>' clus_in ; \ RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \ $INTERACTIVE \ -pwdnamatrix=$PWDNAMATRIX \ -pwgapopen=$PWGOP -pwgapext=$PWGEP \ -type=DNA -transweight=$TRANSWEIGHT \ -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \ -dnamatrix=$DNAMATRIX; \ cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \ RM_LOCAL_FILES(clus_in* TmpInputFile)) itemhelp:clustalw.help // parameters for pairwise alignment: arg:PWDNAMATRIX argtype:choice_menu arglabel:Weighting matrix (pairwise ali) argchoice:IUB:IUB argchoice:CLUSTALW:CLUSTALW arg:PWGOP argtype:slider arglabel:Gap Open Penalty argmin:0 argmax:100 argvalue:15 arg:PWGEP arglabel:Gap Extend Penalty argtype:slider argmin:0 argmax:10 argvalue:6.66 // parameters for multiple alignment: arg:DNAMATRIX argtype:choice_menu arglabel:Weighting matrix (multiple ali) argchoice:IUB:IUB argchoice:CLUSTALW:CLUSTALW arg:GOP argtype:slider arglabel:Gap Open Penalty argmin:0 argmax:100 argvalue:15 arg:GEP arglabel:Gap Extend Penalty argtype:slider argmin:0 argmax:10 argvalue:6.66 arg:MAXDIV arglabel:% identity for delay argtype:slider argmin:0 argmax:100 argvalue:30 arg:TRANSWEIGHT arglabel:Transition weight argtype:slider argmin:0.0 argmax:1.0 argvalue:0.5 arg:INTERACTIVE arglabel:Interactive argtype:choice_menu argchoice:No: argchoice:Yes:-interactive in:TmpInputFile informat:flat insave: out:TmpOutputFile outformat:flat outaligned:yes // -------------------------------------------------------------------------------- item:ClustalW Protein Alignment (fast) seqtype: A itemmeta: o itemmethod:(GOTO_LOCAL_DIR; \ tr '"%//' '>' clus_in ; \ RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \ -quicktree $INTERACTIVE \ -ktuple=$KTUPLE -topdiags=$TOPDIAGS \ -window=$WINDOW -pairgap=$PAIRGAP \ -score=$SCORE \ -type=PROTEIN -transweight=$TRANSWEIGHT \ -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \ -matrix=$MATRIX $NEGMATRIX; \ cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \ RM_LOCAL_FILES(clus_in* TmpInputFile)) itemhelp:clustalw.help // parameters for fast pairwise alignment: arg:PAIRGAP arglabel:Gap penalty (pairwise ali) argtype:slider argmin:1 argmax:500 argvalue:3 arg:KTUPLE arglabel:K-tuple size argtype:slider argmin:1 argmax:2 argvalue:1 arg:TOPDIAGS arglabel:No. of top diagonals argtype:slider argmin:1 argmax:50 argvalue:5 arg:WINDOW arglabel:Window size argtype:slider argmin:1 argmax:50 argvalue:5 // parameters for multiple alignment: arg:MATRIX argtype:choice_menu arglabel:Weighting matrix (multiple ali) argchoice:Gonnet series:GONNET argchoice:Blosum series:BLOSUM argchoice:PAM series:PAM argchoice:ID matrix:ID arg:GOP argtype:slider arglabel:Gap Open Penalty argmin:0 argmax:100 argvalue:10 arg:GEP arglabel:Gap Extend Penalty argtype:slider argmin:0 argmax:10 argvalue:0.2 arg:MAXDIV arglabel:% identity for delay argtype:slider argmin:0 argmax:100 argvalue:30 arg:TRANSWEIGHT arglabel:Transition weight argtype:slider argmin:0.0 argmax:1.0 argvalue:0.5 arg:NEGMATRIX arglabel:Use negative matrix argtype:choice_menu argchoice:No: argchoice:Yes:-negative arg:INTERACTIVE arglabel:Interactive argtype:choice_menu argchoice:No: argchoice:Yes:-interactive in:TmpInputFile informat:flat insave: out:TmpOutputFile outformat:flat outaligned:yes // -------------------------------------------------------------------------------- item:ClustalW Protein Alignment (slow & accurate) seqtype: A itemmeta: l itemmethod:(GOTO_LOCAL_DIR; \ tr '"%//' '>' clus_in ; \ RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \ $INTERACTIVE \ -pwmatrix=$PWMATRIX \ -pwgapopen=$PWGOP -pwgapext=$PWGEP \ -type=PROTEIN -transweight=$TRANSWEIGHT \ -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \ -matrix=$MATRIX $NEGMATRIX; \ cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \ RM_LOCAL_FILES(clus_in* TmpInputFile)) itemhelp:clustalw.help // parameters for pairwise alignment: arg:PWMATRIX argtype:choice_menu arglabel:Weighting matrix (pairwise ali) argchoice:Gonnet series:GONNET argchoice:Blosum series:BLOSUM argchoice:PAM series:PAM argchoice:ID matrix:ID arg:PWGOP argtype:slider arglabel:Gap Open Penalty argmin:0 argmax:100 argvalue:10 arg:PWGEP arglabel:Gap Extend Penalty argtype:slider argmin:0 argmax:10 argvalue:0.1 // parameters for multiple alignment: arg:MATRIX argtype:choice_menu arglabel:Weighting matrix (multiple ali) argchoice:Gonnet series:GONNET argchoice:Blosum series:BLOSUM argchoice:PAM series:PAM argchoice:ID matrix:ID arg:GOP argtype:slider arglabel:Gap Open Penalty argmin:0 argmax:100 argvalue:10 arg:GEP arglabel:Gap Extend Penalty argtype:slider argmin:0 argmax:10 argvalue:0.2 arg:MAXDIV arglabel:% identity for delay argtype:slider argmin:0 argmax:100 argvalue:30 arg:TRANSWEIGHT arglabel:Transition weight argtype:slider argmin:0.0 argmax:1.0 argvalue:0.5 arg:NEGMATRIX arglabel:Use negative matrix argtype:choice_menu argchoice:No: argchoice:Yes:-negative arg:INTERACTIVE arglabel:Interactive argtype:choice_menu argchoice:No: argchoice:Yes:-interactive in:TmpInputFile informat:flat insave: out:TmpOutputFile outformat:flat outaligned:yes