Drupal 7. Replacing core links with their aliases in theme templates
Not sure if this is what you're after, but
in your tpl.php file you can change

&lt;a href="node/1"&gt;Contact&lt;/a&gt;


to

&lt;a href="&lt;?php print url('node/1');?&gt;"&gt;Contact&lt;/a&gt;