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BEGIN { $ENV{CLUSTALDIR} = 'C:/path/to/clustalw1.8/'; }

    my $commandstring = $self->executable." $command"." $instring".
        " -output=$output". " $param_string";
...
    $self->debug( "clustal command = $commandstring");
    my $status = system($commandstring);
    $self->throw( "Clustalw call ($commandstring) crashed: $? \n") unl
+ess $status==0;

sub program_dir {
  return Bio::Root::IO->catfile($ENV{CLUSTALDIR}) if $ENV{CLUSTALDIR};
}

# You will need to enable Clustalw to find the clustalw program. This
# can be done in (at least) two ways:
...
# 2. include a definition of an environmental variable CLUSTALDIR in
# every script that will use Clustal.pm.
# $ENV{CLUSTALDIR} = '/home/peter/clustalw1.8/';