diff --git a/README.md b/README.md
index 3cd1f32..ffbe208 100644
--- a/README.md
+++ b/README.md
@@ -167,6 +167,13 @@ Set custom files and entire folders to ignore within your `/docs` folder. For fi
 		}
 	}
 
+###Disabling clean URLs
+By default, Daux.io will create clean url's that do not include index.php. On servers running Apache, uploading the included .htaccess file should be enough for them to work properly. On servers that are not running Apache or that do not allow custom .htaccess files, you may need to disable clean_urls:
+
+	{
+		"clean_urls": false
+	}
+
 ## Running Remotely
 
 Copy the files from the repo to a web server that can run PHP 5.3 or greater.
diff --git a/docs/00_Getting_Started.md b/docs/00_Getting_Started.md
index 3cd1f32..ffbe208 100644
--- a/docs/00_Getting_Started.md
+++ b/docs/00_Getting_Started.md
@@ -167,6 +167,13 @@ Set custom files and entire folders to ignore within your `/docs` folder. For fi
 		}
 	}
 
+###Disabling clean URLs
+By default, Daux.io will create clean url's that do not include index.php. On servers running Apache, uploading the included .htaccess file should be enough for them to work properly. On servers that are not running Apache or that do not allow custom .htaccess files, you may need to disable clean_urls:
+
+	{
+		"clean_urls": false
+	}
+
 ## Running Remotely
 
 Copy the files from the repo to a web server that can run PHP 5.3 or greater.
diff --git a/libs/functions.php b/libs/functions.php
index ab6b437..72f91d9 100644
--- a/libs/functions.php
+++ b/libs/functions.php
@@ -39,6 +39,7 @@ function get_options() {
 		'twitter' => array(),
 		'links' => array(),
 		'colors' => false,
+		'clean_urls' => true,
 		'google_analytics' => false,
 		'piwik_analytics' => false,
         'ignore' => array()
@@ -228,8 +229,9 @@ function get_ignored() {
 	return $all_ignored;
 }
 
-function get_tree($path = '.', $clean_path = '', $title = ''){
-	$tree = array();
+function get_tree($path = '.', $clean_path = '', $title = '', $first = true){
+    $options = get_options();
+    $tree = array();
     $ignore = get_ignored();
     $dh = @opendir($path);
     $index = 0;
@@ -252,9 +254,29 @@ function get_tree($path = '.', $clean_path = '', $title = ''){
 
      	// Check that this file or folder is not to be ignored
         if(!in_array($file, $ignore)) {
-        	$full_path = "$path/$file";
-        	$clean_sort = clean_sort($file);
-        	$url = $clean_path . '/' . $clean_sort;
+            $full_path = "$path/$file";
+            $clean_sort = clean_sort($file);
+
+            // If clean_urls is set to false and this is the first branch of the tree, append index.php to the clean_path.
+
+            print_r($options['clean_urls']);
+
+            if($options['clean_urls'] == false)
+            {
+                if($first)
+                {
+                    $url = $clean_path . '/index.php/' . $clean_sort;
+                }
+                else
+                {
+                    $url = $clean_path . '/' . $clean_sort;
+                }
+            }
+            else
+            {
+            	$url = $clean_path . '/' . $clean_sort;
+            }
+
         	$clean_name = clean_name($clean_sort);
 
         	// Title
@@ -273,7 +295,7 @@ function get_tree($path = '.', $clean_path = '', $title = ''){
             		'path' => $full_path,
             		'clean' => $clean_sort,
             		'url' => $url,
-            		'tree'=> get_tree($full_path, $url, $full_title)
+            		'tree'=> get_tree($full_path, $url, $full_title, false)
             	);
             } else {
             	// File