X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Faptx%2Faptx_configuration_files%2F_aptx_configuration_file_1;h=075f547afaf824e49688f38cf4370478f274bbd5;hb=5a98ba0564ac9c6d08e00d16319a774ea3a99d05;hp=8b413052417f0ed1ccce6a0e77d1f44f957aac89;hpb=dd8e6f3ab54507a5e4f1e66b3270eb6946cee5d7;p=jalview.git

diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1
index 8b41305..075f547 100644
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1
@@ -125,7 +125,6 @@ font_family:                               Arial,Helvetica,Verdana,Tahoma,Dialog
 font_size:                                 10
 antialias_screen:                          yes
 show_scale:                                yes
-show_branch_length_values:                 no
 cladogram_type:                            ext_node_sum_dep
 phylogeny_graphics_type:                   rectangular
 node_label_direction:                      horizontal
@@ -144,8 +143,10 @@ 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
+right_align_domain_architectures:          no
 branch_length_value_digits:                3
-confidence_value_digits:                   3
+confidence_value_digits:                   2
 background_gradient:                       no
 allow_editing:                             yes
 ext_descendents_data_to_return_on:         window
@@ -199,10 +200,12 @@ show_taxonomy_common_names:     nodisplay no
 show_taxonomy_images:           nodisplay no
 show_annotations:               nodisplay no
 write_confidence_values:        display   ?
+write_branch_length_values:     display   no
 write_events:                   nodisplay no
 use_visual_styles:              display   no
 width_branches:                 display   no
 show_domain_architectures:      nodisplay no
+show_msa:                       nodisplay no
 show_binary_characters:         nodisplay no
 show_binary_character_counts:   nodisplay no
 display_internal_data:          display   yes
@@ -244,9 +247,9 @@ default_click_to: display_node_data
 
 display_color: background                 0x000000
 display_color: background_gradient_bottom 0x0000FF
-display_color: sequence                   0xDCDCDC
+display_color: sequence                   0xE6E6E6
 display_color: taxonomy                   0xB4B4B4
-display_color: confidence                 0x38B0DE
+display_color: confidence                 0xB4B4B4
 display_color: branch_length              0x8C8C8C
 display_color: branch                     0xFFFFFF
 display_color: node_box                   0xFFFFFF
@@ -257,7 +260,8 @@ display_color: matching_a_and_b           0xFFFF00
 display_color: duplication                0xFF0000
 display_color: speciation                 0x00FF00
 display_color: duplication_or_specation   0xFFFF00
-display_color: domains                    0x7B68EE
+display_color: domain_label               0xE6E6E6
+display_color: domain_base                0x646464
 display_color: binary_domain_combinations 0x4169FF
 display_color: annotation                 0xADFF2F
 display_color: overview                   0x828282
@@ -317,7 +321,6 @@ 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
@@ -332,21 +335,23 @@ species_color: DANRE        0x0000BB
 species_color: TETNG        0x0000AA
 species_color: ORYLA        0x000088
 species_color: GASAC        0x000066
-species_color: CAEEL        0xA0A0A0
+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
-species_color: NEMVE        0xAABADD
-species_color: HYDAT        0x7C9BCF
+species_color: NEMVE        0x0066CC
+species_color: HYDAT        0x3399FF
+species_color: HYDVU        0x3399FF
 species_color: LUBBA        0xF7B5CB
 species_color: GEOCY        0xF5A0BD
+species_color: AMPQE        0x009966
 species_color: SUBDO        0xC790B9
 species_color: MONBE        0xFC0FC0
-species_color: DICPU        0x23238E
-species_color: DICDI        0x4D4DFF
+species_color: DICPU        0xFFCC33
+species_color: DICDI        0xFFCC00
 species_color: ENTHI        0x5959AB
 species_color: ARATH        0x00FF00
 species_color: POPTR        0x006400
@@ -381,7 +386,7 @@ 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