#----------------------------   Clustalw  -----------------------------------
item:Clustal alignment
itemmethod:(tr '%#' '>'<in1>clus_in;clustalw -$KTUP -$WIN -$Trans -$FIXED -$FLOAT -$REPORT -output=PIR -infile=clus_in -align  > in1.rpt;sed "s/>DL;/#/g" < clus_in.pir> in1;$REPORT gde in1;/bin/rm -f clus_in* in1*   )&

itemhelp:clustal_help

arg:KTUP
argtype:slider
arglabel:K-tuple size for pairwise search
argmin:1
argmax:10
argvalue:2

arg:WIN
argtype:slider
arglabel:Window size
argmin:1
argmax:10
argvalue:4

arg:Trans
argtype:chooser
arglabel:Transitions weighted?
argchoice:Yes:/TRANSIT
argchoice:No:

arg:FIXED
argtype:slider
arglabel:Fixed gap penalty
argmin:1
argmax:100
argvalue:10

arg:FLOAT
arglabel:Floating gap penalty
argtype:slider
argmin:1
argmax:100
argvalue:10

arg:REPORT
argtype:chooser
arglabel:View assembly report?
argchoice:No:
argchoice:Yes:kedit in1.rpt&

 
in:in1
informat:flat
insave: