DATASET_TANGLEGRAM
#In tanglegrams, an additional tree is displayed next to the main tree. Matching leaf nodes (or nodes specified in the DATA section below) are connected with lines
#lines starting with a hash are comments and ignored during parsing
#=================================================================#
#                    MANDATORY SETTINGS                           #
#=================================================================#
#select the separator which is used to delimit the data below (TAB or SPACE).This separator must be used throughout this file. COMMA cannot be used in this dataset, since it is used within the TANGLEGRAM_TREE
SEPARATOR TAB
#SEPARATOR SPACE

#label is used in the legend table (can be changed later)
DATASET_LABEL	example_tanglegram

#dataset color (can be changed later)
COLOR	#00ff00

#The tree which will be displayed next to the main tree. Put the complete tree text between the fields TANGLEGRAM_TREE and END_TANGLEGRAM_TREE. It can be in Newick, Nexus or phyloXML format, and can contain additional metadata as for standard iTOL trees.
#Its IDs which exactly match the main tree IDs will be automatically connected.
#Additional connections (between non-matching nodes) can be defined below in the DATA section 

TANGLEGRAM_TREE

#((((((Thalassiosira_pseudonana:0.33483,
#(Cryptosporidium_hominis:0.25048,
#Plasmodium_falciparum:0.28267)Apicomplexa:0.14359[100])Eukaryota:0.03495[42],
#((Cyanidioschyzon_merolae:0.38319)Eukaryota:0.08133[96],
#(Dictyostelium_discoideum:0.34685,(((Eremothecium_gossypii:0.07298,Saccharomyces_cerevisiae:0.07619)Saccharomycetaceae:0.21170[100],Schizosaccharomyces_pombe:0.24665)Ascomycota:0.15370[100],(((Diptera:0.10724)Diptera:0.09870[100],((Takifugu_rubripes:0.03142)Actinopterygii:0.04335[100],(((Rattus_norvegicus:0.03107)Murinae:0.00398[91],(Homo_sapiens:0.00957,Pan_troglodytes:0.03864)Hominidae:0.01549[100])Euarchontoglires:0.01629[99],Gallus_gallus:0.04596)Gnathostomata:0.01859[100])Gnathostomata:0.09688[100])Metazoa:0.03693[95],(Caenorhabditis_elegans:0.01843,Caenorhabditis_briggsae:0.01896)Caenorhabditis:0.24324[100])Metazoa:0.09911[100])Eukaryota:0.04004[85])Eukaryota:0.02708[41])Eukaryota:0.02636[44])Eukaryota:0.06455[87],
#Leishmania_major:0.45664)Eukaryota:0.10129[100],Giardia_lamblia:0.55482)Eukaryota:0.57543[100]):0.88776);

END_TANGLEGRAM_TREE


#=================================================================#
#     all other optional settings can be set or changed later     #
#           in the web interface (under 'Datasets' tab)           #
#=================================================================#

#Each dataset can have a legend, which is defined using LEGEND_XXX fields below
#For each row in the legend, there should be one shape, color and label.
#Optionally, you can define an exact legend position using LEGEND_POSITION_X and LEGEND_POSITION_Y. To use automatic legend positioning, do NOT define these values
#Optionally, shape scaling can be present (LEGEND_SHAPE_SCALES). For each shape, you can define a scaling factor between 0 and 1.
#To order legend entries horizontally instead of vertically, set LEGEND_HORIZONTAL to 1
#Shape should be a number between 1 and 6, or any protein domain shape definition.
#1: square
#2: circle
#3: star
#4: right pointing triangle
#5: left pointing triangle
#6: checkmark
#7: solid line
#8: dashed line
#9: dotted line

#LEGEND_TITLE	Dataset legend
#LEGEND_SCALE	1
#LEGEND_POSITION_X	100
#LEGEND_POSITION_Y	100
#LEGEND_HORIZONTAL	0
#LEGEND_SHAPES	1	2	3
#LEGEND_COLORS	#ff0000	#00ff00	#0000ff
#LEGEND_LABELS	value1	value2	value3
#LEGEND_SHAPE_SCALES	1	1	0.5


#style for the default connections between the leaves (normal, dashed or dotted)
DEFAULT_CONNECTION_STYLE	normal

#default connection color (hex, RGB or RGBA notation)
DEFAULT_CONNECTION_COLOR	#888888

#default connection width in pixels
DEFAULT_CONNECTION_WIDTH	1

#margins between the end of leaf labels/tree nodes and the start/end of the connection line
CONNECTION_MARGIN_RIGHT	0
CONNECTION_MARGIN_LEFT	0

#starts and ends of the connections will have a straigt line of this length
CONNECTION_TAIL	0 

#connections will be curved
CONNECTION_CURVE	1 

#maximum connection width specified in the DATA section will be drawn with this value. All other widths will be scaled down proportionally
MAXIMUM_LINE_WIDTH	1

#display the leaf labels on the tanglegram tree
SHOW_LABELS	1

#leaf label size factor
SIZE_FACTOR	1

#leaf label shift in pixels (positive or negative), relative to the tanglegram tree
LABEL_SHIFT	0

#alignment of the tanglegram leaf labels (left or right), relative to the tanglegram tree
LABEL_ALIGN	right

#pan the tanglegram tree horizontally and/or vertically 
TREE_PAN_H	0
TREE_PAN_V	0

#tanglegram tree scaling factors, horizontal and vertical
TREE_SCALE_H	1
TREE_SCALE_V	1

#=================================================================#
#       Actual data follows after the "DATA" keyword              #
#=================================================================#

DATA

#In the DATA section, several types of annotations can be specified. The type is defined in the first field, and can be 'connect' or 'style'

#By using the 'connect' annotation, additional connections between non-matching leaves can be defined, or non-default styles for matching leaf connections

#Each line defines a single connection between 2 leaves and consists of the following fields:
#connect MAIN_TREE_NODE_ID TANGLEGRAM_TREE_NODE_ID WIDTH COLOR STYLE LABEL

#Only the leaf IDs are required. You can also specify the same ID in both trees, when a specific, non-default style should be used for that particular connection
#All connection widths will be normalized based on the MAXIMUM_LINE_WIDTH specified for the whole dataset
#STYLE defines the connection line style, and can be one of 'normal', 'dashed' or 'dotted'.
#color can be specified in hexadecimal, RGB or RGBA notation
#label will be shown in the mouseover info popup, if defined

#connect	Giardia_lamblia	Giardia_lamblia	4	#ff0000	dotted	test label
#connect	Homo_sapiens	Homo_sapiens	2	#0000ff	normal	Human label
#connect	Drosophila_melanogaster	Diptera	1	#00ff00	dashed	Diptera links
#connect	Anopheles_gambiae	Diptera	1	#00ff00	dashed	Diptera links


#By using the 'style' keyword in the first field, you can define branch/label styles for the tanglegram tree.
#The format is identical to the main "Branch and label styles" dataset, check the 'dataset_styles_template.txt' file for complete details
#Note that you can use the last common ancestor method to define internal tanglegram tree nodes as well (check the help page for details)

#Each line defines a style to be applied, and consists of the following fields:
#style,TANGLEGRAM_TREE_NODE_ID,TYPE,WHAT,COLOR,WIDTH_OR_SIZE_FACTOR,STYLE,BACKGROUND_COLOR


#Homo sapiens node will have its label displayed in blue with bold italic font, and with yellow background

#style	Homo_sapiens	label	node	#0000ff	1	bold-italic	#ffff00

#Metazoa clade starting at the last common ancestor of Caenorhabditis_elegans and Homo_sapiens will have all its branches colored green

#style	Caenorhabditis_elegans|Homo_sapiens	branch	clade	#00ff00	1	normal