--- a/reprof.xml	Mon Nov 30 20:10:58 2015 -0500
+++ b/reprof.xml	Wed Dec 02 15:01:36 2015 -0500
@@ -54,6 +54,28 @@
 Three states of secondary structure are predicted: helix (H; includes alpha-,
 pi- and 3_10-helix), (beta-)strand (E = extended strand in beta-sheet
 conformation of at least two residues length) and loop (L).
+
+Protein Classification
+----------------------
+
+Proteins can be classified as mixed given the following classes:
+
+-  'all-alpha': %H > 45% AND %E < 5%
+-  'all-beta': %H < 5% AND %E > 45%
+-  'alpha-beta': %H > 30% AND %E > 20%
+-  'mixed': All others
+
+Gff3 Data and Evidence Codes
+----------------------------
+
+In order to facilitate interoperability with other downstream analyses, and to
+document provenance, the Galaxy tool author has opted to apply ECO:0000255 to
+all annotated features in the GFF3 file. Per the `UniPro Evidence page <http://www.uniprot.org/help/evidences#ECO:0000255>`__
+
+    The ECO code ECO:0000255 is also used for information which has been
+    generated by various sequence analysis programs that are used during the
+    manual curation process and which has been verified by a curator.
+
       ]]></help>
   <citations>
     <citation type="doi">10.1186/1471-2105-10-S13-O3</citation>