# 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'
+# To extract UniProt taxonomy codes (e.g. CAEEL) or UniProt identifiers (or scientific names)
+# from node names during NH/NHX/Nexus file parsing: 'taxonomy_extraction_in_nh_parsing'
+# possible values are:
+# 'no'
+# 'pfam_strict' (for e.g. MOUSE from BCL2_MOUSE/23-453, or [uniprot] 10090 from BCL2_10090/23-453)
+# 'pfam_relaxed' (for e.g. MOUSE from bax_MOUSE, or [uniprot] 10090 from bax_10090)
+# 'aggressive' (for e.g. MOUSE from MOUSE, or [uniprot] 10090 from 10090, or Nematostella vectensis from xyz_Nematostella_vectensis)
#
# Internal node labels are confidence values during NH/NHX/Nexus file parsing:
# 'internal_labels_are_confidence_values', possible values are 'yes', 'no'
default_node_size: 4
default_node_shape: rectangle
default_node_fill: solid
-taxonomy_colorize_node_shapes: no
#graphics_export_x: 595
#graphics_export_y: 792
pdf_export_line_width: 0.5
# NH/NHX/Nexus file parsing:
internal_labels_are_confidence_values: no
replace_underscores_in_nh_parsing: no
-taxonomy_extraction_in_nh_parsing: pfam
+taxonomy_extraction_in_nh_parsing: pfam_relaxed
click_to: sort_descendants display
click_to: color_subtree display
click_to: open_seq_web nodisplay
+click_to: open_pdb_web nodisplay
click_to: open_tax_web nodisplay
click_to: blast nodisplay
click_to: cut_subtree nodisplay
display_color: branch 0xFFFFFF
display_color: node_box 0xFFFFFF
display_color: collapsed 0xFFFF00
-display_color: matching_nodes 0x00FF00
+display_color: matching_a 0x00FF00
+display_color: matching_b 0xFF0000
+display_color: matching_a_and_b 0xFFFF00
display_color: duplication 0xFF0000
display_color: speciation 0x00FF00
display_color: duplication_or_specation 0xFFFF00