X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Faptx%2Faptx_configuration_files%2F_aptx_configuration_file;h=ac5a9350130b8d85c4b7682e10234bbaac6bb3d2;hb=5a98ba0564ac9c6d08e00d16319a774ea3a99d05;hp=b2dfd95b641f71accc425bfc8263b79715f4ef7d;hpb=50d5287a84926572394575b36a47fa0f62c84bcd;p=jalview.git

diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
index b2dfd95..ac5a935 100644
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
@@ -168,6 +168,7 @@ phylogeny_graphics_type:                   rectangular
 node_label_direction:                      horizontal
 show_default_node_shapes_internal:         no
 show_default_node_shapes_external:         no
+show_node_shapes_for_nodes_with_vis_data:  yes 
 default_node_size:                         4
 default_node_shape:                        rectangle
 default_node_fill:                         solid
@@ -181,7 +182,7 @@ overview_placement_type:                   upper_left
 color_labels_same_as_branch_length_values: no
 display_sequence_relations:                no
 show_domain_labels:                        yes
-line_up_renderable_data:                   no
+line_up_renderable_data:                   yes
 right_align_domain_architectures:          no
 show_seq_annotation_ref_sources:           yes
 branch_length_value_digits:                3
@@ -370,7 +371,6 @@ species_color: CIOSA        0xFF2CAE
 species_color: BOVIN        0x5C3317
 species_color: CANFA        0x8B2323
 species_color: HUMAN        0xFF2400
-species_color: Homo_sapiens 0xFF2400
 species_color: PANTR        0xCC2400
 species_color: MOUSE        0xFF7F00
 species_color: RAT          0xFFEF00
@@ -385,10 +385,10 @@ species_color: DANRE        0x0000BB
 species_color: TETNG        0x0000AA
 species_color: ORYLA        0x000088
 species_color: GASAC        0x000066
-species_color: CAEEL        0x666666
+species_color: CAEEL        0x666699
 species_color: CAEBR        0xB0B0B0
-species_color: DROME        0x706F00
-species_color: DROPS        0x504F00
+species_color: DROME        0x663366
+species_color: DROPS        0x996699
 species_color: APIME        0x7A7700
 species_color: AEDAE        0x8C5900
 species_color: TRICA        0x918E00
@@ -397,7 +397,7 @@ species_color: HYDAT        0x3399FF
 species_color: HYDVU        0x3399FF
 species_color: LUBBA        0xF7B5CB
 species_color: GEOCY        0xF5A0BD
-species_color: AMPQE        0x0099FF
+species_color: AMPQE        0x009966
 species_color: SUBDO        0xC790B9
 species_color: MONBE        0xFC0FC0
 species_color: DICPU        0xFFCC33
@@ -436,7 +436,7 @@ species_color: mammals        0xFF0000
 species_color: Chordata       0x8470FF
 species_color: Echinodermata  0x6495ED
 species_color: Hemichordata   0x7EC0EE
-species_color: Arthropoda     0x7AC5CD 
+species_color: Arthropoda     0x7AC5CD
 species_color: Nematoda       0x7171C6
 species_color: Tardigrada     0x388E8E
 species_color: Annelida       0xC67171