# Example: 'node_label_direction: horizontal'
# The two possible values are: horizontal
# radial
-# Show default node shape: 'show_default_node_shapes': values: 'yes'/'no'
+# Show default node shape for internal nodes: 'show_default_node_shapes_internal': values: 'yes'/'no'
+# Show default node shape for external nodes: 'show_default_node_shapes_external': values: 'yes'/'no'
# Default node shape size: 'default_node_size'
# Example: 'default_node_size: 6'
# Default node shape type: 'default_node_shape'
# sequence_name
# sequence_acc
# sequence_mol_seq
+# sequence_mol_seq_fasta
# sequence_symbol
# taxonomy_scientific_name
# taxonomy_code
min_confidence_value: 0.0
font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
font_size: 10
+font_size_min: 2
+font_size_max: 20
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
-show_default_node_shapes: no
-default_node_size: 6
-default_node_shape: circle
-default_node_fill: gradient
+show_default_node_shapes_internal: no
+show_default_node_shapes_external: 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
background_gradient: no
allow_editing: yes
ext_descendents_data_to_return_on: window
-ext_descendents_data_to_return: user_selected
+ext_descendents_data_to_return: sequence_mol_seq_fasta
#label_for_get_ext_descendents_data: Get_Node_Data
# NH/NHX/Nexus file parsing:
internal_labels_are_confidence_values: no
replace_underscores_in_nh_parsing: no
-taxonomy_extraction_in_nh_parsing: pfam
-
-
-
-# Initial Window Size for Application and ArchaeopteryA applet
-# ------------------------------------------------------------
-window_initial_size_x: 800
-window_initial_size_y: 800
-
+taxonomy_extraction_in_nh_parsing: yes
# Checkbox Display Selection
show_binary_character_counts: display no
display_internal_data: display yes
dynamically_hide_data: display yes
-show_relation_confidence: display no
+show_relation_confidence: display no
show_properties: display no
show_vector_data: display no
-# Web Links
-# ---------
-# Format: web_link: <URL> <description> <source identifier>
-# E.g. "http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB"
-# <description> is not used at the moment.
-# <source identifier> corresponds to the <source> element for <sequence> <accession>,
-# and to the <type> of <taxonomy> <id> (see www.phyloxml.org).
-
-web_link: http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB
-web_link: http://www.uniprot.org/uniprot/?query= SPTREMBL sptrembl
-web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= NCBI GI
-web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= RefSeq RefSeq
-web_link: http://www.ebi.ac.uk/interpro/IEntry?ac= InterPro InterPro
-web_link: http://www.rcsb.org/pdb/explore.do?structureId= PDB PDB
-web_link: http://pfam.sanger.ac.uk/protein?entry= Pfam pfam
-web_link: http://tolweb.org/ ToL tol
-web_link: http://www.eol.org/pages/ EOL eol
-web_link: http://www.uniprot.org/taxonomy/ UniProt-Taxonomy uniprot
-web_link: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id= NCBI-Taxonomy ncbi
-web_link: http://www.ubio.org/browser/details.php?namebankID= uBio namebankID
-# not working at the moment:
-web_link: http://www.ensembl.org/Homo_sapiens/Search/Summary?species=all;idx=;q= Ensembl Ensembl
-
-
-
-# Settings Specific for ArchaeopteryxE
-# ------------------------------------
+# Settings Specific for Archaeopteryx Applets (E and A)
+# -----------------------------------------------------
+# To automatically midpoint reroot trees upon loading: 'midpoint_reroot: yes'
+
+midpoint_reroot: yes
+
+
+
+# Settings Specific for ArchaeopteryxE Applets
+# --------------------------------------------
# To hide controls and menus: 'hide_controls_and_menus: yes'
# To use tabbed display : 'use_tabbed_display: yes'
default_number_of_bootstrap_resamples: 100
mafft_local: /bin/mafft
-clustalo_local: C:\Users\zma\SOFTWARE\clustal-omega-1.1.0-win32\clustalo.exe
fastme_local: /bin/fastme
raxml_local: /bin/raxml