item:ClustalW automatic itemmeta: W 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/^\*$//g" >out1; )); \ RM_LOCAL_FILES(clus_in* in1)) itemhelp:clustalw.help in:in1 informat:flat insave: out:out1 outformat:flat // -------------------------------------------------------------------------------- item:Create ClustalW Profile 2 itemmeta: C itemmethod:(GOTO_LOCAL_DIR ; tr '"%//' '>' ../clus_prf ; RM_LOCAL_FILES(in1)) itemhelp:clustalw.help in:in1 informat:flat insave: // -------------------------------------------------------------------------------- item:ClustalW Profile Alignment itemmeta: P itemmethod:(GOTO_LOCAL_DIR; \ tr '"%//' '>' clus_in; \ RUN_IN_WINDOW((clustalw -output=PIR -profile1=clus_in -profile2=../clus_prf -align ; \ cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >out1; )); \ RM_LOCAL_FILES(clus_in* in1)) itemhelp:clustalw.help in:in1 informat:flat insave: out:out1 outformat:flat // -------------------------------------------------------------------------------- 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=$DNAMATRIX; \ cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >out1; )) ; \ RM_LOCAL_FILES(clus_in* in1)) 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:in1 informat:flat insave: out:out1 outformat:flat // -------------------------------------------------------------------------------- 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=$DNAMATRIX; \ cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >out1; )) ; \ RM_LOCAL_FILES(clus_in* in1)) 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:in1 informat:flat insave: out:out1 outformat:flat // -------------------------------------------------------------------------------- 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 $NEGMATRIX; \ cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >out1; )) ; \ RM_LOCAL_FILES(clus_in* in1)) 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:in1 informat:flat insave: out:out1 outformat:flat // -------------------------------------------------------------------------------- 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 $NEGMATRIX; \ cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >out1; )) ; \ RM_LOCAL_FILES(clus_in* in1)) 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:in1 informat:flat insave: out:out1 outformat:flat // -------------------------------------------------------------------------------- item:Assemble Contigs itemmeta: g itemmethod: ( GOTO_LOCAL_DIR; \ tr '"%//' '>' in1.tmp; \ CAP2 in1.tmp $OVERLAP $PMATCH > out1; \ RM_LOCAL_FILES(in1 in1.tmp) ) itemhelp:CAP2.help arg:OVERLAP argtype:slider arglabel:Minimum overlap? argmin:5 argmax:100 argvalue:20 arg:PMATCH argtype:slider arglabel:Percent match required within overlap argmin:25 argmax:100 argvalue:90 in:in1 informat:flat out:out1 outformat:gde