Now that part is bug in the module, its using string form of system, which is subject to shell interpolation, can be fixed like 

##      my $commandstring = $self->executable."$instring"."$param_stri
+ng";
##        $commandstring .= ' 1>/dev/null' if $quiet;
##        $self->debug( "clustal command = $commandstring");
##        
##        my $status = system($commandstring);
          my @command = ( $self->executable, $instring, $param_string 
+);
        $self->debug( "clustal command = @command ");
        
        my $status = system(@command);

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In reply to Re^11: Can't run Clustalw through Bioperl by Anonymous Monk
in thread Can't run Clustalw through Bioperl by dimitris852

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