I think what you want is to use a php include. It allows you to have a common part of your site (e.g. like the nav, or the footer) in a separate file and you can just 'include' it into all of your other files. I may have misinterpreted what you meant, sorry if I have.
<!-- nav.php -->
<ul>
<li><a href="#">Some Link</a></li>
....
<li><a href="#">Some Link</a></li>
</ul>
//index.php
<html>
<head>
</head>
<body>
<?php include('nav.php'); ?>
</body>
</html>
//sub-page.php
<html>
<head>
</head>
<body>
<?php include('nav.php'); ?>
</body>
</html>
