-# To replace underscores with spaces during NH/NHX/Nexus file parsing (application only):
-# 'replace_underscores_in_nh_parsing'
-# To extract taxonomy codes from Pfam-style sequence labels (e.g. 'QW231_HUMAN/129-694')
-# during NH/NHX/Nexus file parsing (application only): 'extract_pfam_tax_codes_in_nh_parsing'
-# Internal node labels are confidence values during NH/NHX/Nexus file parsing (application only):
-# 'internal_labels_are_confidence_values'
+#
+# NH/NHX/Nexus file parsing
+# -------------------------
+# To replace underscores with spaces during NH/NHX/Nexus file parsing:
+# 'replace_underscores_in_nh_parsing', possible values are 'yes', 'no'
+#
+# To extract UniProt taxonomy codes (e.g. CAEEL) from node names during NH/NHX/Nexus file parsing:
+# 'taxonomy_extraction_in_nh_parsing',
+# possible values are 'yes' (for e.g. BCL2_MOUSE), 'pfam' (for e.g. BCL2_MOUSE/23-453), 'no'
+#
+# Internal node labels are confidence values during NH/NHX/Nexus file parsing:
+# 'internal_labels_are_confidence_values', possible values are 'yes', 'no'
+
+
+
+# phyloXML parsing
+# ----------------
+# To ensure compatibility with all current and future
+# phyloXML applications and to detect malformatted and
+# possibly erroneous data, it is strongly recommended
+# to enable validation of all phyloXML files
+# against the XSD Schema (see: http://www.phyloxml.org/),
+# with:
+# 'validate_against_phyloxml_xsd_schema: true'
+
+validate_against_phyloxml_xsd_schema: true