Help and FAQs
We tested the following:
- Linux/Unix: Chrome, Firefox and Opera work fine with Flash 7 plugin.
- Windows: Microsoft Internet Explorer 7 or later, Chrome, Firefox and Opera work fine. Due to many security problems and ActiveX bugs, we do not recommend Internet Explorer. Version 6 of Internet Explorer is not supported at all.
- Mac: Chrome, Firefox, Opera and Safari all work without problems.
iTOL's branch pruning, rerooting and collapsing functions allow you to customize the tree however you like. These functions are performed by clicking the left mouse button on any branch or leaf. You will get a popup window showing the available functions, depending on the current status of the node. You can also use the shortcuts mentioned in the function descriptions below. Remember to click the 'Update tree' button after you are finished with pruning/collapsing the nodes.
All these functions are non-destructive, meaning you can always go back to the original tree by clicking the 'Reset tree' button.
Pruning and collapsing (click to enlarge)
- export the current tree into any of the following formats: Portable Network Graphics (png), Encapsulated Postscript (eps), Postscript (ps), Portable Document Format (pdf), Scalable Vector Graphics (svg), Newick (txt) or Nexus (txt). If you plan to include the tree in a publication, we recommend exporting to a 150 or 300 DPI png image. To further edit the tree in a vector based editing software (like Adobe Illustrator or Inkscape), use either svg or eps. Adobe Illustrator sometimes has problems with svg, so we recommend eps when using Illustrator. For best results and greatest amount of control, we recommend exporting to svg and using Inkscape to edit and convert the file.
- download the multiple sequence alignment used to create the current tree (if available). It the tree is pruned, the alignment will contain only those species which are present in the pruned tree. You can choose clustal, phylip or FASTA as alignment output formats.
Note about transparency
If you use transparency in your datasets (for example in pie charts or connections), the only way to preserve it in the exported trees is to use either svg or png format. Exporting to pdf goes through an intermediary eps file, and transparency is not suppored by eps or ps.
In addition to the Tree Of Life and other precomputed trees available through the 'Other trees' page, you can upload and display your own trees.
To upload a tree, go to the 'Data upload' page. Your tree should be in a plain text file, and in any of the supported formats (Newick, Nexus or PhyloXML).
Example trees in Newick format:
|Tree with bootstraps and branch lenghts||Tree with internal node IDs|
(A:0.1,(B:0.1,C:0.1)90:0.1)98:0.3); A, B, C : leaf names 0.1, 0.3 : branch lenghts 90,98 : bootstrap values
(A:0.1,(B:0.1,C:0.1)INT1:0.1)INT2:0.3); A, B, C : leaf names INT1, INT2 : internal node IDs 0.1, 0.3 : branch lenghts 90,98 : bootstrap values
When uploading a tree, you can optionally upload extra data for display on it. Unless you have a personal account in iTOL, the datasets must be uploaded together with the tree, at the same time. Otherwise, you can add or remove datasets from a tree through the tree and dataset function popups in your account (see account help for details). Up to 10 sets of data can be displayed on one tree. Each dataset should be in a separate plain text file. All fields should be separated using the same separator (you can choose space, comma or tab character). First field on each line should be a node ID (or an ID pair, see 'Defining names for internal nodes' below), followed by the actual data value(s).
iTOL can display the following types of data:
Nodes of the tree have either zeroes or ones associated with them. Each value will be represented with a square, white for zeroes and your selected color for ones. Values for internal nodes will only be displayed on collapsed clades.
If multiple binary datasets are added to a tree, they will be automatically prevented from overlapping, allowing simultaneous display of several datasets.
Gallus_gallus,1 Rattus_norvegicus,1 Mus_musculus,0 Homo_sapiens,1 Pan_troglodytes,0
Simple bar charts
Nodes have a single value associated with them. Highest value in the dataset is shown as a bar with the selected maximum pixel size, and others are adjusted proportionally to it. Bars will be filled with the color you selected during upload. Values for internal nodes will only be displayed on collapsed clades.
Simple bar charts support scales, as described in the 'Dataset scales' section below.
Gallus_gallus,50 Rattus_norvegicus,10 Mus_musculus,75 Homo_sapiens,100 Pan_troglodytes,90
Multi-value bar charts
Nodes have multiple values (up to a 100) associated with them. Node with the highest sum of values will be represented with a bar with the selected maximum pixel size, and all other values will be adjusted based on it. Values for internal nodes will only be displayed on collapsed clades. First line of the dataset file must contain the labels for individual fields (first field of the line should be LABELS, followed by the actual labels). Labels will be shown when hovering mouse cursor over the bars in the graphical display, and used to display a separate legend in the exported tree images. Second line can be used to define the colors for individual fields (optional; first field should be COLORS, followed by color definitions in standard hexadecimal RGB notation).
Multi value bar charts support scales, as described in the 'Dataset scales' section below.
LABELS,mylabel_1,mylabel_2,mylabel_3 COLORS,#ff0000,#00ff00,#0000ff Gallus_gallus,20,20,20 Rattus_norvegicus,50,10,75 Mus_musculus,100,50,20 Homo_sapiens,75,50,10 Pan_troglodytes,20,20,50
|If 'Align individual fields' is selected during upload, each field's start will be aligned based on the maximum values of previous fields.||Graphical representation:|
Input file is almost identical to the 'Multi-value bar charts' described above, and follows the same rules. The important difference is that you can associate data with internal tree nodes. Internal nodes can be defined in two ways:
- If your tree has proper IDs associated with internal nodes (see the first section of 'Uploading and working with your own trees' section), you can use these directly.
- Use two leaf IDs separated with a vertical line (|), whose last common ancestor will be used as the internal node (see the example below).
In addition to standard data points for each node, first field after the node ID is used to define the radius of the pie chart (in format R + numeric value, for example R50). Values for all the radii defined will be normalized according to the values selected during upload ('Min. radius' and 'Max. radius' pixel values). If radius is not defined, data will be displayed as a multi-value bar, using the rules defined above (always visible for leaves, and visible only on collapsed internal nodes; in the example below, Gallus gallus and Pan troglodytes have radii defined, so their data is displayed as a pie chart).
Actual position of the pie chart on the branch can also be specified as a percentage of the node's total branch length. This optional value can be added after the radius value, separated with a vertical line. Value of 0 translates into the start of the branch, while 1 translates into the end. The default value is 0.5 (ie. the middle of the branch). In the example below, Gallus_gallus has the pie chart position specified as 1.0 ('R50|1.0'), which puts it at the very end of the branch. On the other hand, position value for Pan_troglodytes is 0.2 ('R50|0.2'), and the pie chart is displayed at 20% of the branch length. Note that position values are not limited to range of zero to one (ie. they can be bigger than one, or negative).
LABELS,test0,test1,test2,test3 COLORS,#ff0000,#00ff00,#0000ff,#ff00ff Gallus_gallus|Homo_sapiens,R50,10,20,20,10 Rattus_norvegicus|Mus_musculus,R100,20,20,20,10 Homo_sapiens|Pan_troglodytes,R50,20,10,10,20 Homo_sapiens|Mus_musculus,R75,10,10,10,10 Homo_sapiens,20,20,20,20 Pan_troglodytes,R50|0.2,20,20,20,20 Mus_musculus,10,20,30,40 Rattus_norvegicus,20,10,40,40 Gallus_gallus,R50|1.0,20,20,20,20
Leaves have a single value associated with them. Each value is converted into a colored box, using the color selected during upload.In addition, you can specify the color in the dataset file, using a line starting with field 'COLOR' and using a color hex code after the separator (for example, "COLOR,#ff00ff"). Highest value in the dataset is displayed using the exact color specified, with lower values gradually fading towards white (for the lowest value in the dataset).
Gallus_gallus,50 Rattus_norvegicus,5 Mus_musculus,20 Homo_sapiens,10 Pan_troglodytes,40
You can define your own colors for each leaf separately. Use standard hexadecimal color notation (for example, #ff0000 for red). Optionally, each leaf can have a text label associated with it. The label, if defined, will appear in a popup window when the mouse pointer is above the corresponding dataset point. Labels should be the 3rd field in the dataset file (in the example below, it would be "Homo_sapiens,#0000ff,MY_LABEL").
In addition, you can use this dataset type to automatically assign colors to tree branches. Ancestral branches whose children have identical colors will be colored as well. In the example below, upload option 'color branches and show boxes' was used (in the Branch coloring section).
Gallus_gallus,#ff0000 Rattus_norvegicus,#00ff00 Mus_musculus,#00ff00 Homo_sapiens,#0000ff Pan_troglodytes,#0000ff
This dataset will provide an animated view of multiple values associated with each leaf (ie. an animated simple bar chart). First line of the dataset file must contain the labels for individual values (first field of the line should be LABELS, followed by the actual labels). Labels will be shown in the animation control box, above the progress bar. Second line can be used to define the colors for individual fields (optional; first field should be COLORS, followed by color definitions in standard hexadecimal RGB notation).
When a time series is displayed in iTOL, you will see a 'Time series control' box, which is used to control the animation. Click the play/pause button to start or stop the animation. You can also drag the progress bar indicator to quickly find a specific field.
Time series datasets support scales, as described in the 'Dataset scales' section below.
LABELS,test0,test1,test2,test3,test4 COLORS,#ff0000,#00ff00,#0000ff,#ff00ff,#ffff00 Gallus_gallus,10,30,20,50,30 Rattus_norvegicus,30,20,40,5 Mus_musculus,20,50,10,30,50 Homo_sapiens,10,30,40,20,40 Pan_troglodytes,30,10,50,20
Protein domain architecture
Each node in the tree can have a protein domain architecture associated with it. Even though it's primary use is for the display of protein domains, it can be used for various other purposes. The format is as follows: Each line should have a node ID, total protein length, and the definitions of the domains. The domain definitions field contains one or more domains, separated using the same character which is used in the first two fields. Each domain definition consists of 5 parts, separated with vertical lines ("|"). For example:
RE|100|150|#ff0000|SH2The fields are:
- RE: 2 character code defining the domain shape (see below for supported shapes)
- 100: domain start position
- 150: domain end position
- #ff0000: color definition (hexadecimal RGB notation)
- SH2: domain label
Supported domain shapes:
|TR||right pointing triangle|
|TL||left pointing triangle|
|PL||left pointing pentagram|
|PR||right pointing pentagram|
|PU||up pointing pentagram|
|PD||down pointing pentagram|
'GP' shape (for 'gap') will be displayed as a 1/3 height rectangle, and it's primary use is for the gaps in the multiple sequence alignments.
Exported trees with a protein domain architecture dataset will contain an additional legend listing all domains and their labels. The legend will not be shown in interactive mode, since you can hover your mouse cursor over any domain to show its label and other associated information. Domain architectures for internal nodes will only be displayed on collapsed clades.
Protein domain arcitectures support scales, as described in the 'Dataset scales' section below.
Gallus_gallus,300,EL|10|50|#ff0000|DUF17,DI|200|290|#aaff00|DUF22 Rattus_norvegicus,360,TR|50|170|#aa00cc|DUF2,TL|175|270|#f044ff|DUF4 Mus_musculus,320,DI|80|190|#f0c0c0|DUF7,EL|175|225|#3400ff|DUF10 Homo_sapiens,350,RE|100|150|#a0faa0|DUF4,HH|250|310|#ffff00|DUF7 Pan_troglodytes,350,HV|20|110|#0043ff|DUF1,EL|125|325|#0dfff0|DUF2
Leaves have multiple values associated with them, which are converted into colors based on gradients selected during upload. You have to select 3 values and their correpsonding color: maximum,minium and midpoint. They don't need to correspond to the actual min and max values in the dataset, and midpoint does not need to be exactly in the middle. These values are used to construct 2 color gradients (from minimum to mindpoint and from midpoint to maximum). Dataset values are then mapped to these gradients to select their color. Each value will be represented with a colored box of the width specified during upload. The whole dataset cannot be wider than 5000 pixels, so pratically the limit is 5000 values per leaf (with 1px box width).
First line of the dataset file must contain the labels for individual fields (first field of the line should be LABELS, followed by the actual labels). Labels will be shown when hovering mouse cursor over the boxes in the graphical display, and used to display a separate legend in the exported tree images.
An optional Newick formated file can be uploaded with the heatmap dataset. Its leaf IDs must exactly match the dataset labels. The tree will be used to sort the dataset fields, and will be displayed above the dataset (in normal display mode only).
LABELS,mylabel_1,mylabel_2,mylabel_3,mylabel_4,mylabel_5,mylabel_6 Gallus_gallus,-10,-5,0,5,-10,15 Rattus_norvegicus,-5,0,5,10,-15,15 Mus_musculus,-20,0,20,30,-25,30 Homo_sapiens,-10,5,15,25,-30,25 Pan_troglodytes,-5,0,10,30,-10,20
|Additional tree file:|
Boxplot datasets can be uploaded in 2 ways:
- Direct upload of five-number summaries and extremes: each leaf has a least 5 values associated with it. Starting from left, the first 6 fields must be: leaf ID, minimum value, lower percentile, median, upper percentile and maximum value. An unlimited number of extra fields can be added, each representing an outlier value (either high or low).
- Upload of raw data: each leaf has at least 4 values associated with it. iTOL will calculate all needed values to display a boxplot for each leaf. You can specify the lower and upper percentile during upload (by default, these will be 25% and 75%). You can also define the step constant, which will be multiplied with each leaf's box size to define the related whisker size. The constant can be any number above zero, and is normally set to 1.5. When uploading raw data, you can also optionally control the drawing of outliers, using the 'Calculate extremes' option in the upload form.
Boxplots support scales, as described in the 'Dataset scales' section below.
In this example, the dataset contains the five-number summary for each leaf, plus several outliers (for Gallus_gallus, Mus_musculus and Pan_troglodytes)
Gallus_gallus,10,15,20,25,30,0,5,60 Mus_musculus,5,20,40,50,60,70,80 Rattus_norvegicus,15,30,40,50,65 Homo_sapiens,10,20,35,50,55 Pan_troglodytes,10,20,40,55,65,80
This dataset type is only available in inverted circular display mode. Any two nodes in the tree (leaves or internal) can be connected with a line of specified width, color and transparency. Additionaly, each connection can have an associated label, which will be shown in the popup window when mouse pointer is hovering above the line. Each line in the dataset must contain the following fields:
NODE_ID_1 NODE_ID_2 LINE_WIDTH LINE_ALPHA LINE_COLOR LABEL
If your tree doesn't have internal node IDs, you can use the last common ancestor method described below, in the 'Defining names for internal nodes' section. LINE_ALPHA defines the transparency of the line (from 0 for fully transparent to 255 for opaque). LINE_COLOR should be in standard hexadecimal color notation (for example #ff0000 is red), and LINE_WIDTH represents the width in pixels (valid range is 1-1000).
Homo_sapiens,Gallus_gallus,10,255,#ff0000,Example connection Anopheles_gambiae,Homo_sapiens|Mus_musculus,50,125,#00ff00,Connection to internal node Mus_musculus,Danio_rerio,5,255,#0000ff,Another leaf to leaf connection Gallus_gallus|Danio_rerio,Anopheles_gambiae|Caenorhabditis_elegans,100,100,#ffff00,Internal to internal Caenorhabditis_elegans,Eremothecium_gossypii,200,55,#00ffff,Connection 5 Schizosaccharomyces_pombe,Caenorhabditis_briggsae,50,100,#ff00ff,Connection 6
Connections example (click to enlarge)
Nodes have multiple values (up to a 50) associated with them. Values will be shown as circles of different radii. Highest value in the dataset will have the largest radius (caluclated based on tree display, depending on available space between the leafs). Radius for the smallest value will be calculated based on the percentage selected in the upload form. Values for internal nodes will only be displayed on collapsed clades.
First line of the dataset file must contain the labels for individual fields (first field of the line should be LABELS, followed by the actual labels). Labels will be shown when hovering mouse cursor over the bars in the graphical display, and used to display a separate legend in the exported tree images. Second line can be used to define the colors for individual fields (optional; first field should be COLORS, followed by color definitions in standard hexadecimal RGB notation). If colors are not defined in the dataset file, all circles will be assigned the same color which was selected in the upload form.
LABELS,label_1,label_2,label_3,label_4,label_5 COLORS,#ff0000,#00ff00,#0000ff,#ff00ff,#ffff00 Gallus_gallus,20,20,30,80,50 Rattus_norvegicus,50,10,75,40,5 Mus_musculus,100,50,20,60,10 Homo_sapiens,75,50,10,70,30 Pan_troglodytes,20,20,50,90,10
Displaying custom scales with datasets
Several dataset types support the display of custom scales: Simple bar chart, Multi value bar chart, Time series, Boxplot and Protein domains. Scales are defined through a separate line on top of the dataset file (or below the LABELS line, if present). The line should start with the field "DATASET_SCALE", followed by a list of values which define where the scale lines will be displayed (see Example 1 below). Optionally, it is possible to define the line color and a label to be displayed with each line (see Example 2 below). Label and color for a scale line are added after the value, separated with dashes:
Use the standard hexadecimal notation for colors, and make sure that the label doesn't contain the separator character.
|1. Multi barchart Dataset file:
LABELS,mylabel_1,mylabel_2,mylabel_3 DATASET_SCALE,10,20,30,40,50 Gallus_gallus,10,10,20 Rattus_norvegicus,5,10,30 Mus_musculus,15,25,30 Homo_sapiens,5,5,35 Pan_troglodytes,10,15,20
|2. Simple barchart dataset file:
DATASET_SCALE,2000-2k line-#0000ff,10000-example 10k-#ff0000,20000 Gallus_gallus,17709 Rattus_norvegicus,22159 Mus_musculus,25307 Homo_sapiens,22287 Pan_troglodytes,21506
Displaying horizontal gene transfers (HGTs) on your tree
iTOL is one of the first tree display tools which can display horizontal gene transfers annotated in the original Newick file, ie. no extra files are necessary. HGT information is included in the IDs of tree nodes. Therefore, in addition to leaf IDs, your tree must have unique IDs assigned to all internal nodes. A valid Newick tree with internal node IDs is shown in the example above (first part of the 'Uploading and working with your own trees' section). In addition to direct annotation in the tree, HGT definitions can also be uploaded in a separate file (listed under 'Advanced options' in the tree upload page).
Annotating HGTs in the Newick tree
HGT information is included in the ID of the originating node. After the ID, first add the keyword #HT# followed with a list of one or mode destination nodes. Separate multiple destinations with a + sign. You can optionally define the color and label for each HGT. Use standard RGB hexadecimal notation (for example, 0xff0000 for red) and put the color after the destination node ID, separated with a | symbol (vertical line). Labels are added in the same way, after the color definition and they will be shown in the popup windows when hovering the mouse pointer over the HGT arrow.
Here are two examples:
|Newick tree:||Graphical representation:|
(A:0.1,(B:0.1,C:0.1)INT1#HT#A:0.1)INT2:0.3);Internal node INT1 is the originating node and leaf A is the destination.
s e p a r a t o r s | | | | | | | | ((A#HT#C:0.1,(B:0.1,C:0.1)INT1:0.1)INT2:0.3,(D:0.1,E:0.2)INT3#HT#B|0xff0000|my_label1+INT1|0x0000ff|my_label2:0.3); | | | | destination 1 destination 2There are 3 HGTs annotated here.
First is a simple one from leaf A to leaf C. Other two are originating from internal node INT3. HGT towards leaf B will be colored red (0xff0000), and the one towards node INT1 will be blue (0x0000ff). Destinations are separated with a + (plus) sign, and colors and labels are separated from destinations with a | (vertical line) sign.
Defining HTGs in a separate file
Alternatively, you can upload HGT definitions in a plain text file by using the advanced upload option 'Horizontal gene transfers'. The file should be tab separated plain text file with the following fields:
SOURCE_NODE_ID DESTINATION_NODE_ID COLOR LABELBoth SOURCE_NODE_ID and DESTINATION_NODE_ID can be either leaf IDs or internal node IDs. If your tree doesn't have internal node IDs, use the last common ancestor method described below, in the 'Defining names for internal nodes' section. For the COLOR field, use standard hexadecimal notation (ie. #ff0000 for red). LABEL is optional, and will be shown in the popup windows when hovering over the HGT arrow.
|HGT definition file:
Gallus_gallus Pan_troglodytes|Homo_sapiens #0000ff fake_transfer_1 Pan_troglodytes|Homo_sapiens Rattus_norvegicus #00ff00 fake_transfer_2 Mus_musculus Gallus_gallus #ff0000 fake_transfer_3
Automatic assignment of species names and taxonomic names for internal nodes
After a sucessful upload, you will get an option of automatic assignment of taxonomy information to your tree. This option will only be available if all leaf IDs in your tree are NCBI species taxonomy IDs. The procedure is as follows:
- For each internal node in the tree, get all leaf IDs
- For each of these leaves, find the lowest common taxonomic classification in the NCBI tree
- If this name is assigned to other internal nodes which are not subnodes of the current node, add the keyword 'subclade'
In addition to the internal nodes, leaf IDs will be changed from taxID into their proper scientific names.
This function can also be accessed through the tree options popup in your personal iTOL account.
Defining color ranges, clade and label colors
You can define clade (branch lines) or label (leaf text label) colors and color ranges using the color editor. After a sucessful upload, one of the links under 'What now?' section will take you to the editor. The editor can also be accessed through the tree options menu in your iTOL account.
Alternatively, you can upload the color definitions in a plain text file by using the advanced upload option 'Color definitions'. The file should be tab separated plain text file with the following fields:
NODE_ID TYPE COLOR LABEL
NODE_ID can be a leaf ID or an internal node ID. If your tree doesn't have internal node IDs, use the last common ancestor method described below, in the 'Defining names for internal nodes' section. TYPE should be either range, label or clade. For the COLOR field, use standard hexadecimal notation (ie. #ff0000 for red). LABEL is used only for color ranges, and will be shown in the legend box. Please note that multiple ranges with identical colors must also have identical labels.
Leaf color ranges on a tree (click to enlarge)
|Color definition file:
Gallus_gallus|Homo_sapiens clade #0000ff no_label Pan_troglodytes|Homo_sapiens clade #00ff00 no_label Mus_musculus|Homo_sapiens range #aaffaa Euarchontoglires Homo_sapiens range #00ff00 important1 Gallus_gallus range #ff0000 important2 Homo_sapiens label #ffff00 Gallus_gallus label #0000ff Pan_troglodytes label #ff0000
Defining font styles for the leaf labels
You can use various font styles (bold, italic or bold-italic) in the leaf labels. These styles will only be used during tree export to graphical file formats. Font style definitions should be uploaded in a separate file, using the file selection box provided below the main tree upload box.
Styles are defined as follows:
- one line per leaf, two fields per line, tab separated
- first field corresponds to a tree leaf ID
- second field defines the font style, using simple tags
Here is an example file:
Homo_sapiens <B>Homo</B> <BI>sapiens</BI> Pan_troglodytes Pan <I>troglodytes</I> Escherichia_coli_K12 <B>Escherichia coli</B> <I>K12</I>In the final tree, these would be displayed as:
Homo sapiens Pan troglodytes Escherichia coli K12
Defining names for internal nodes
To define names for internal nodes in your tree, you can upload an extra file (using the 'Names for internal nodes' field on the upload page).
Names are defined in the file as follows:
- one line per leaf, two fields per line, tab separated
- first field defines the internal node:
- directly, using an ID (if your tree has proper internal node IDs assigned)
- using two leaf IDs separated with a vertical line (|), whose last common ancestor will be used as the internal node
- second field defines the name of the internal node
|Name definition file:
Gallus_gallus|Homo_sapiens Gnathostomata Mus_musculus|Homo_sapiens Euarchontoglires Homo_sapiens|Pan_troglodytes Hominidae
In this example
Defining clades which will be collapsed by default
If you are working with very large trees, you can upload a file with a set of internal node IDs which should be collapsed by default. The IDs should be on separate lines in the file (ie. one ID per line), and can either be direct internal node IDs (if your tree has them), or you can define them by using two leaf IDs for which that node is the last common ancestor (see the details in the section above, 'Defining names for internal nodes'). For the example tree above, if your pre-collapsed clades file contains only the line:
the node INT2 will be collapsed by default.
Defining node labels
iTOL can display custom labels next to any node in the tree. Each labels' color and text can be separately defined and uploaded through the 'Branch labels' field in the 'Advanced options' part of the upload page. The file should be in plain text, with each line containing 3 tab-separted fields:
NODE_ID BRANCH_LABEL_TEXT BRANCH_LABEL_COLOR
When specifying information for internal nodes, you can either use the exact internal node IDs (if your tree uses them), or you can define them using the last common ancestor (see the details in the section 'Defining names for internal nodes' above). Colors should be in standard hexadecimal notation (for example, #ff0000 for red).
|Branch labels file:
Gallus_gallus|Homo_sapiens Gnathostomata Mus_musculus|Homo_sapiens Euarchontoglires Homo_sapiens|Pan_troglodytes Hominidae
Defining custom information for node popups
Custom information for the node popup windows can be uploaded by using the 'Popup box info' field in the 'Advanced options' part of the upload page. The file should be in plain text, with each line containing 3 tab-separted fields:
NODE_ID POPUP_TITLE_TEXT POPUP_HTML_CONTENT
When specifying information for internal nodes, you can either use the exact internal node IDs (if your tree uses them), or you can define them using the last common ancestor (see the details in the section Defining names for internal nodes' above). For the popup content, only a few basic HTML tags are supported (limited by Flash). Please use only double quotes in the HTML definition. See the sample file below for some examples.
In addition to the HTML content and popup titles, you can define the Cascading Style Sheets which will be applied to each popup box. Cascading style sheet definitions should be included at the top of the file. First field must contain the keyword CSS followed with a tab character and the actual style definition.
Note about including external images:
Only JPEG and GIF formats are supported. Due to weird Flash problems, you should use the following format to properly display the image:
<textformat tabstops="[IMAGE_WIDTH]"> <img src="http://IMAGE_URL" height="IMAGE_HEIGHTpx" width="IMAGE_WIDTHpx" /> \t </textformat>
Replace IMAGE_WIDTH, IMAGE_HEIGHT and IMAGE_URL with the correct values.
The sample popup shown on the right was defined using this example file. Note that you can "invent" new tags for styling (for example, tag box in the definition file).
Customized popup window:|
If you are using iTOL to upload and display your own trees, you can create a personal iTOL account. It will allow you to access your trees from anywhere, organize them into workspaces and projects and easily manage datasets and other tree features. Your trees are kept private and stored localy in iTOL. You can easily share your trees with others by sending them a link to your tree in iTOL.
Detailed help and explanation of user account features is avaliable on a separate page.
Advanced users are encouraged to use iTOL batch access capabilities for large scale tree upload and export. The interfaces are described in detail on a separate page, together with example upload and download scripts.
- How can I get branch lengths and/or bootstraps on a tree created using your NCBI tree generator?
You cannot. These trees simply represent a pruned version of NCBI taxonomy in Newick format, nothing more. Proper phylogenetic tree reconstruction methods must be used to get branch lengths and bootstrap values.
- Why is transparency lost when exporting trees to PDF?
Export to PDF goes through an intermediary EPS file, and EPS does not support transparency. Please use SVG or PNG instead.