sub writeXML()          # HTML code
{

  my $output = new IO::File(">comOutput/$newRefFile.xml");
  my $writer = new XML::Writer(OUTPUT => $output);
  
  $writer->xmlDecl();
  $writer->startTag("Main");
  
  $writer->startTag("NewHits");
   # write only the new hits to the file
  foreach my $element(@newHits)
  {
    $writer->startTag( "GI" );
	  $writer->dataElement( "GI" , $element);
	  $writer->endTag( "GI" );
    $writer->startTag("E-value");
    $writer->dataElement( "E-value" , $evals{$element});
    $writer->endTag("E-value");
    $writer->startTag("Score");
    $writer->dataElement( "Score" , $newScores{$element});
    $writer->endTag("Score");
  }
  $writer->endTag("NewHits");
  $writer->endTag("Main");
  $writer->end();
  $output->close();
}