-<p>Jalview can read alignment files in any of the following formats:</p>\r
-<p><em>Fasta , MSF, Clustal, BLC, PIR, MSP, PFAM </em></p>\r
-<p>Use the menu at the top of the main application window to read in files from\r
-</p>\r
+<p>Jalview can read alignment files in any of the following standard formats:</p>\r
+<p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm</em></p>\r
+<p>The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a> of\r
+ these file formats.</p>\r
+<p>Additionally, annotated whole sets of alignments and trees can be\r
+read from a <a href="../features/jalarchive.html">Jalview (jar)\r
+format</a> file using <strong>Desktop→Load\r
+Project</strong>. </p>\r
+<p>Use the <strong>Desktop→Input Alignment</strong> menu to read in files from:</p>\r