<script type="text/javascript">
function checkboxes(elm) {
  var checkboxes = 0;
  for (i=0; i<elm.alignment_seq.length; i++){
    if (elm.alignment_seq[i].checked==true) {
	  checkboxes++;
	  break;
	}
  }
  if (!checkboxes) {
	alert("Keine Checkbox aktiviert!");
	return false;
  }
  return true;
}
</script>

<form name="testformular" action="alig.pl" method="get" onsubmit="return checkboxes(this)">
<input type="checkbox" name="alignment_seq" value="a">
<input type="checkbox" name="alignment_seq" value="b">
<input type="submit" value="c">
</form>