diff --git a/Makefile b/Makefile
index e620a7db..87f0f3a4 100644
--- a/Makefile
+++ b/Makefile
@@ -51,8 +51,9 @@ OVERRIDES = \
 .PHONY: lib clean purge 
 
 # if you change all: make sure all: in standard.mk is consistent.
+# api-doc target must be run last.
 
-all: installdirs $(TOOL_HDR) lib 
+all: installdirs $(TOOL_HDR) lib api-doc
 
 # Use the PACKAGES macro to transform lib, bin, etc., targets
 # into package level dependencies, e.g., lib -> PkgA.lib, PkgB.lib
@@ -67,7 +68,8 @@ purge:
 	rm -rf $(TARGET) bin/*.r 
 
 api-doc:
-	perl src/WebApplication/scripts/api2html.pl -url http://api.metagenomics.anl.gov -outfile site/CGI/Html/api.html
+	perl src/WebApplication/scripts/api2html.pl -url http://api.metagenomics.anl.gov/beta -site_name "MG-RAST" -outfile site/CGI/Html/api.html
+	perl src/WebApplication/scripts/api2html.pl -url http://kbase.us/services/communities/beta -site_name "Microbial Communities" -outfile site/CGI/Html/api.kbase.html
 
 ##
 # Targets to setup the expected directory structure for the
diff --git a/src/MGRAST/cgi/api2.cgi b/src/MGRAST/cgi/api2.cgi
index 43dd13cd..124029a1 100644
--- a/src/MGRAST/cgi/api2.cgi
+++ b/src/MGRAST/cgi/api2.cgi
@@ -33,6 +33,13 @@ if ($abs !~ /\.cgi/) {
 }
 my $rest = $cgi->url(-path_info=>1);
 $rest =~ s/^.*$abs\/?//;
+$rest =~ s/^\///;
+$rest =~ s/^\d+//;
+$rest =~ s/^beta//;
+$rest =~ s/^\///;
+$rest =~ s/^api2\.cgi//;
+$rest =~ s/^\///;
+
 my @rest_parameters = split m#/#, $rest;
 map {$rest[$_] =~ s#forwardslash#/#gi} (0 .. $#rest);
 
@@ -177,11 +184,14 @@ if ($resource) {
 }
 # we are called without a resource, return API information
 else {
-  my @resource_objects = map { { 'name' => $_, 'url' => $cgi->url.'/'.$_ } } sort @$resources;
+  my $cgi_url = $cgi->url;
+  $cgi_url =~ s/^(.*)\/$/$1/;
+  $cgi_url =~ s/^(.*)\/api2.cgi$/$1/;
+  my @resource_objects = map { { 'name' => $_, 'url' => $cgi_url.'/'.$_ } } sort @$resources;
   my $content = { version => 1,
 		  service => 'MG-RAST',
 		  url => $cgi->url,
-		  documentation => $cgi->url.'/api.html',
+		  documentation => $cgi_url.'/api.html',
 		  description => "RESTful Metagenomics RAST object and resource API\nFor usage note that required parameters need to be passed as path parameters, optional parameters need to be query parameters. If an optional parameter has a list of option values, the first displayed will be used as default.",
 		  contact => 'mg-rast@mcs.anl.gov',
 		  resources => \@resource_objects };
diff --git a/src/WebApplication/scripts/api2html.pl b/src/WebApplication/scripts/api2html.pl
index 2e2e71bf..30cae982 100755
--- a/src/WebApplication/scripts/api2html.pl
+++ b/src/WebApplication/scripts/api2html.pl
@@ -12,17 +12,19 @@
 
 sub usage {
   print "api2html.pl >>> create an HTML API documentation file from a REST API\n";
-  print "api2html.pl -url <url to api> -outfile <file for html output>\n";
+  print "api2html.pl -url <url to api> -site_name <name of site> -outfile <file for html output>\n";
 }
 
 # read in parameters
-my $url     = '';
-my $outfile = '';
+my $url       = '';
+my $site_name = '';
+my $outfile   = '';
 
 GetOptions ( 'url=s' => \$url,
+             'site_name=s' => \$site_name,
 	     'outfile=s' => \$outfile );
 
-unless ($url and $outfile) {
+unless ($url and $site_name and $outfile) {
   &usage();
   exit 0;
 }
@@ -58,7 +60,7 @@ sub usage {
 $structure->{resources} = $resources;
 
 # start the template
-my $html = template_start();
+my $html = template_start($site_name);
 
 # build the navigation
 $html .= '<li><a href="#overview">overview</a></li>';
@@ -70,7 +72,7 @@ sub usage {
     <div class="span12" style="margin-left: 270px;">
 ~;
 
-$html .= "<h1><a name='overview' style='padding-top: 50px;'>".$structure->{service}->{name}." Overview</a></h1><p>".$structure->{service}->{description}."</p><hr>";
+$html .= "<h1><a name='overview' style='padding-top: 50px;'>".$site_name." Overview</a></h1><p>".$structure->{service}->{description}."</p><hr>";
 
 my %param_types = ( body => "<p>This parameter must be passed in the message body.</p>",
                     options => "<p>This is an optional parameter and may be passed in the query string.</p>",
@@ -113,6 +115,10 @@ sub usage {
             }
         }
         $html .= "</ul>";
+        if (exists $req->{example}) {
+            $html .= "<h3>Example</h3><ul>";
+            $html .= "<li>".$req->{example}[0]."<li>".$req->{example}[1]."</ul>";
+        }
         $html .= "<h3>Return Attributes</h3><ul>";
         # iterate over attributes
         foreach my $param (sort keys(%{$req->{attributes}})) {
@@ -188,11 +194,12 @@ sub usage {
 exit;
 
 sub template_start {
+  my $site_name = shift;
   return qq~
 <!DOCTYPE html>
 <html>
   <head>
-    <title>MG-RAST API</title>
+    <title>$site_name API</title>
     <meta http-equiv="content-type" content="text/html; charset=utf-8" />
     <script type="text/javascript" src="bootstrap.min.js"></script>
     <link rel="stylesheet" type="text/css" href="bootstrap.min.css" />
@@ -202,7 +209,7 @@ sub template_start {
     <div class="navbar navbar-inverse navbar-fixed-top">
       <div class="navbar-inner">
 	<div class="container">
-	  <a class="brand" href="./index.html">MG-RAST API documentation</a>
+	  <a class="brand" href="./index.html">$site_name API documentation</a>
 	</div>
       </div>
     </div>