my $infile = "homologene1.fa";
my $pid = open2(*Reader, *Writer, "clustalw") or die "Cant open clustalw: $!\n";
Writer->autoflush();
Reader->autoflush();
STDIN->autoflush();

print Writer "1\n";
print Writer "$infile\n";
print Writer "2\n";
print Writer "9\n";
print Writer "4\n";
print Writer "\n";
print Writer "\n";
print Writer "1\n";
print Writer "\n";
print Writer "\n";
print Writer "\n";
# <----- i need to wait here before making more user input
print Writer "x\n";
print Writer "\n";
print Writer "x\n";
close(Writer);
close(Reader);
waitpid($pid, 0);