function myTheme_menu_tree($variables) {
  return '<nav class="menu">' . $variables['tree'] . '</nav>';
}

// for admin menu
<?php print '<ul id="nav-admin" class="menu clearfix">'.menu_tree('navigation').'</ul>';?>

// for primary menu
 <?php print  '<ul id="nav-primary" class="menu clearfix">' . menu_tree('primary-links').'</ul>'; ?>

// for secondary menu
 <?php print  '<ul id="nav-secondary" class="menu clearfix">' . menu_tree('secondary-links').'</ul>'; ?>

function yourthemename_menu_tree($tree) {
  return $tree;
}