Version history

Version 6.9.1

• Multi font styles can be defined through an annotation file, or interactively for individual labels
• Automatic taxonomy assignment is possible on any tree. An annotation file can be used to specify the taxonomy IDs for leaf nodes.
• Bulk editing supports label filtering
• Node ID display can be limited to certain classes only

Version 6.9

• In Heatmap datasets, several types of data normalization can be performed
• In Heatmap datasets, numeric values can be displayed directly on the heatmap
• Several dataset types support automatic label color calculation based on the darkness of the backround (Heatmaps, Colored strips, Colored/labeled ranges and Shape plots

Version 6.8.2

• Dataset legends can be individualy scaled

Version 6.8.1

• Dataset legends can be automatically generated from the dataset information
• Batch deletion interface available for removal of individual trees or complete projects
• In Colored/labeled ranges, vertical spacing between ranges or brackets can be added

Version 6.8

• Colored/labeled ranges datasets are supported in the web dataset editor

Version 6.7.6

• Node metadata can be updated or added by using the METADATA template file
• Node metadata can be updated or added through the iTOL annotation editor

Version 6.7.5

• External services can be used for iTOL sign in and new account creation (via Google or Microsoft accounts)
• Dataset legend fields can be reordered by dragging the rows in the web legend editor

Version 6.7.4

• In Colored/labeled ranges datasets, ranges can be manually extended/reduced on the right/left
• Multi font style label creator now works directly with the original tree labels
• Multi font style label creator can define separate font family and fine-tune the position of each label part

Version 6.7.3

• Node metadata can be edited or added interactively via the metadata editor

Version 6.7.2

• Bulk editing of tree labels via several functions
• Automatic creation of text label datasets to display multi font style labels

Version 6.7.1

• Custom labels available in simple bar charts, which can be displayed instead of values
• Custom position and style can be defined for value labels in simple bar charts

Version 6.7

• New dataset type: Colored/labeled ranges
• Legacy colored ranges can be automatically converted to a dataset

Version 6.6

• Automatic taxonomy assignment is possible for trees using GTDB accession numbers as leaf IDs
• Custom classes can be specified for internal tree nodes
• Clades can be automatically collapsed based on node classes

Version 6.5.8

• Dataset legend entries can be displayed horizontally

Version 6.5.7

• Leaf sort order of the complete tree can be inverted

Version 6.5.6

• In multiple sequence alignment datasets, consensus sequence calculation threshold can be specified
• Detailed residue distribution is displayed in multiple sequence alignment information popups

Version 6.5.5

• Multiple sequence alignment datasets support proper highlighting of residues as dots. Residues can be compared to the alignment consensus sequence or to one or more reference sequences. When defined, reference sequences can be highlighted with user styled boxes.

Version 6.5.4

• Border style can be set on bootstrap/metadata display symbols
• Customizable background boxes can be displayed behind bootstrap/metadata text labels, branch length labels and internal node ID labels

Version 6.5.3

• Support for export of all node metadata in text modes (Newick, NEXUS) in various formats
• Sorting of nodes in Newick and NEXUS exported trees mirrors the interactive display

Version 6.5.2

• Pie chart datasets can be displayed as polar area diagrams

Version 6.5.1

• Color gradient dataset legend can be automatically generated
• internal node IDs/labels can be displayed directly on the branches

Version 6.5

• vertical spacing factor can be set individually for each leaf node

Version 6.4.3

• public access to each individual tree can be restricted ( icon in the user account tree tables)

Version 6.4.2

• improved shape calculation of clade colored ranges in unrooted mode, with an extra option to smooth the range borders

Version 6.4.1

• support for LibreOffice Calc in the iTOL annotation editor
• support for branch styling during upload directly from phyloXML embedded annotations (color and width)
• when present, branch colors and width factors are exported in phyloXML format

Version 6.4

• Multiple styles can be used within a single text label (bold, italic, color, font family, superscript, subscript)

Version 6.3.3

• Branch symbols can be filled with color gradients
• rotation of individual branch symbols is now consistent across all display modes

Version 6.3.2

• datasets legend can be sorted by drag/dropping individual datasets. The dataset order is saved with tree views.
• tree node hover information popups can be disabled through the personal settings menu ( icon in the control panel header)

Version 6.3.1

• when symbols are used in automatically generated metadata legends, their size will exactly match the current tree display

Version 6.3

• Substring matching available in template files (with full Regex support), allowing the assignment of annotations to multiple matching nodes
• Tree nodes can be automatically marked with symbols (with independent styles for leaves and internal nodes)
• Colored strip datasets support the display of individual text labels inside each colored box. Colored strips can have borders displayed on all sides.

Version 6.2

• manually collapsed nodes can be exported into a COLLAPSE template file
• when displaying metadata, multiple thresholds can be defined simultaneously (if multiple metadata sources are present)
• when displaying the internal tree scale in time scale mode, labels can be rounded to a set number of decimals
• dataset legend shapes can be inverted, ie. drawn with a colored border and without fill

Version 6.1.2

• Automatic clade collapsing and branch deletion can be used on multi-bootstrap trees, or trees with extended node metadata

Version 6.1.1

• Bootstrap/metadata symbols and labels correctly positioned over curved branches
• Branch symbols dataset correctly positioned over curved branches

Version 6.1

• Clipboard pasting supported in the web dataset editor
• Clades can be automatically collapsed based on bootstrap values

Version 6

• Complete rewrite and modernization of the user interface, personal account page and the web dataset editor
• Various columns in the user account project displays can be reordered and switched on/off, with per project or account wide settings
• Default position for various user interface panels can be defined
• Undo menu implemented, allowing quick reversal of several editing and annotation functions
• Midpoint rooting is available directly from the tree display page
• When displaying metadata as branch widths, the default width can be set (for nodes not matching the selected metadata range)
• In phylogenetic placements datasets, removed the limit on the number of node matching sequences that can be searched (tested with several hundred thousands)
• In external shape datasets, the style of grid lines and value labels can be defined
• In branch symbol datasets, border style for the symbols can be defined
• In boxplot datasets, border style for the plots can be defined
• In gradient datasets and colored strips, the dataset label can be displayed above the strip
• Field labels above various datasets (e.g. heatmaps) can be rotated and shifted
• Collapsed clade labels can be individually edited and styled
• Label font size can be locked to a user specified value
• Leaf-to-label connections can be solid or dashed lines
• Range metadata type from MrBayes trees can be displayed as text labels or branch colors
• Due to frequent system overloads, a queueing system was implemented for the figure export
• New help pages with integrated video tutorials

Version 5.7

• In connections datasets, connections within a single node are displayed as loops of variable size.
• Text label datasets are supported in the unrooted display mode. External labels can be shifted horizontally.
• Tree scale box is fully customizable, and can be disabled. Label text and size can be changed, as well as line color and width. A fixed value for the scale can be forced (so the scale value doesn't change with zooming).
• Tree edits (moving/deleting nodes or clades) can be simply undone though a function in the Save/restore view function menu

Version 5.6.3

• Multiple bootstrap / metadata values can be displayed simultaneously as text labels

Version 5.6.2

• Individual projects can be privately shared with your collaborators. Check the Sharing data page for more details.

Version 5.6.1

• Legend position can be specified in the dataset templates
• Legends can be dragged and repositioned

Version 5.6

• In dataset legends, size of individual shapes can be defined
• Dashed lines can be displayed between leaf labels and external datasets

Version 5.5.1

• In text label datasets, internal labels can be positioned above or below the branch labels, and their position fine tuned
• An automatically generated legend can be added to the tree when support values/metadata are visualized as symbols or branch colors

Version 5.5

• New dataset type: MEME motifs (created automatically from MEME suite XML files)

Version 5.4

• Equal-daylight layout available in unrooted display mode

Version 5.3

• expanded manual annotation tools:
  • undo function replaced with delete tool, so any object can be individually deleted
  • polygon tool now supports curves, so any shape can be drawn
  • path/shape editing tool added, allowing individual path points to be moved, and curves adjusted

Version 5.2

• color gradients can be used for tree branches
• vertical shift and font color can be specified for branch length and metadata text labels

Version 5.1.1

• in heatmap datasets, cell border color and width can be specified
• fill color for collapsed clade shapes can be specified
• border width and style for collapsed shapes follow the underlying node

Version 5.1

• width and color can be specified for dashed lines connecting leaves with labels
• manual annotation / drawing tools: a set of very basic drawing tools allowing direct manual annotation of trees

Version 5

• complete rewrite and optimization of iTOL's underlying drawing code, which uses paper.js now
• support for high resolution screens, resulting in increased display sharpness
• tree branches can be displayed as curves
• full support for gradient fills in exported figures (protein domains)
• internal tree scale lines can be dashed, and displayed in different widths
• optimized clade collapsing, fixing the overlap of collapsed clades
• collapsed clade triangle width can be changed in unrooted display mode

Version 4.4.2

• Dataset scales now support custom display labels with variable size. Scale lines can be dashed, and displayed in different widths.

Version 4.4.1

• Support for non-numeric node metadata in NHX and MrBayes trees. Non-numeric categories can be visualized as branch colors or as text labels.
• Bootstraps and other numeric metadata can be displayed as percentages and scaled by any factor

Version 4.4

• internal scale can be displayed at user defined fixed positions, in addition to intervals
• internal scale can be shown as an axis, grid or both
• internal scale can be customized to show any values, not only branch lengths, by specifying the root value and scaling factor

Version 4.3.3

• support for dashed lines in Connections datasets

Version 4.3.2

• new annotation file: prune.txt, allowing simple tree pruning with a list of IDs

Version 4.3.1

• Leaf labels can be aligned on the right side, towards the datasets.
• Font size can be set for internal tree scale labels.
• Branch/label styles datasets supported in batch mode
• Node information shown when hovering over residues in multiple sequence alignments

Version 4.3

• Tree views can be saved as defaults for the complete projects.

Version 4.2.4

• Added support for QIIME 2 FeatureData[AlignedSequence] QZA files, which create multiple sequence alignment datasets

Version 4.2.3

• Legends can be defined for Branch/label styles datasets

Version 4.2.2

• Protein domain datasets are supported in unrooted display mode
• Automatic leaf label rotation can be switched off in circular and unrooted display modes

Version 4.2.1

• Connection datasets are supported in unrooted display mode
• Field labels can be displayed in External shapes datasets

Version 4.2

• New dataset type: Branch/label styles (dataset_styles_template.txt)
• Automatic color legend can be generated in Phylogenetic placements datasets, when summary type is set to 'Branch color'

Version 4.1.1

• Leaf label background colors can be defined, both interactively, and through the TREE_COLORS annotation files.

Version 4.1

• Initial support for QIIME 2 QZA files. QZA trees can be uploaded directly.
• QZA taxonomy files dropped onto the tree will automatically assign leaf labels and create a bar chart with confidence values
• QZA FeatureTable[Frequency] supported

Version 4.0.3

• In Binary datasets, symbols can be aligned to the ends of leaf labels. Individual dataset fields will not be aligned to each other in this case.

Version 4.0.2

• In Text labels datasets, labels can be displayed without rotation (ie. making them always appear straight)
• In Image datasets, individual images will be properly aligned on all sides of the tree.

Version 4.0.1

• Dataset legends and scales can be created and edited directly in the iTOL web interface

Version 4.0

• Datasets can now be created and edited directly in the iTOL web interface, without using external text templates. A simple spreadsheet interface is used to enter the data. Full details are available in the help pages and in the corresponding tutorial video.
• Full support for the majority of Google Web Fonts. New fonts can be enabled by using the 'Add' button next to Label font selector.
• Removed TRANSPARENT_FILL option from 'Shape plot' datasets, since FIELD_COLORS now support full RGBA color specification
• Check marks can be used in branch symbol datasets

Version 3.6.1

• UTF-8 characters can be used in all annotation files (for example α or β can be used in labels and elsewhere)
• Multi-bootstrap values (separated with forward slashes; for example ones generated by IqTree) will be automatically parsed into separate metadata sources and available for visualization

Version 3.6

• Position of the branch length labels can be adjusted
• Node ages can be displayed instead of raw branch length values
• Position of the bootstrap/metadata symbols and text labels can be adjusted

Version 3.5.4

• Colored ranges legend is sortable
• Support for custom color schemes in alignments

Version 3.5.3

• Leaf sorting and node rotation supported in unrooted mode
• Colored ranges properly cover clades in unrooted mode

Version 3.5.2

• Slanted (triangular) display mode available

Version 3.5.1

• internal tree scale can be inverted (starting from the longest leaf, instead of the tree root)

Version 3.5

• New dataset type: Images (dataset_image_template.txt)
• in Heatmap datasets, the color for the null fields (specified using the 'X' character in the data) can be changed

Version 3.4.3

• line chart datasets can have custom titles (see the updated dataset_linechart_template.txt)

Version 3.4.2

• added support for visualizing metadata from MrBayes and NHX

Version 3.4.1

• Binary, branch symbols and internal piechart datasets are supported in unrooted display mode

Version 3.4

• New dataset type: Line charts (dataset_linechart_template.txt)

Version 3.3.3

• Last tree access and last tree modification times are shown in the project tree tables
• Project tree tables can be quickly sorted on any column
• Information on workspace/project and last restored view name are displayed in the tree info popups

Version 3.3.2

• Multiple sequence alignment datasets accept unprocessed FASTA alignments (it is no longer required to put sequences into a single line and remove space characters)

Version 3.3.1

• The size of collapsed nodes can be proportional to the number of leaves within them
• Any node's child leaf labels can be copied to the system clipboard

Version 3.3

• colored ranges can be displayed with borders of different widths/colors
• colored ranges can cover the complete tree
• Bootstrap and branch length text labels can be rounded or displayed in scientific notation

Version 3.2.4

• New dataset type: Multiple sequence alignment (dataset_alignment_template.txt)
• Label size for heatmap and binary datasets can be changed independently
• Added the function to remove all branches below specified bootstrap value

Version 3.2.3

• border width and color can be set for simple barcharts, multi bar charts and pie charts
• new features in the protein domains dataset:
  • border width and color can be set for individual domain shapes
  • backbone height can be changed
  • domains can be filled with plain colors or gradients

Version 3.2.2

• new annotation file: collapse.txt, allowing simple collapsing of multiple clades

Version 3.2.1

• Leaf label position can be adjusted (Label shift option)
• Dashed lines connecting leaves to labels can be disbaled
• Internal circle symbols can be displayed on all nodes, nodes with one child only or hidden completely

Version 3.2

• Heatmap dataset legend automatically created
• Heatmap dataset values corresponding to minimum, midpoint and maximum colors can be freely changed
• 'Duplicate tree' function available in the personal account

Version 3.1.1

• Copy shared trees into personal account

Version 3.1

• Batch access available
• Better reporting of errors during upload
• Datasets:
  • New dataset type: phylogenetic placements
  • Labels can be displayed above binary dataset columns
  • Connections dataset lines can be curved towards center and aligned to labels
  • Domain dataset labels font size factor implemented
• Search your account trees from any page (magnifying glass in the header)
• Navigation to other project trees in the tree viewer header
• Many bug fixes

Version 3

• Complete, from-scratch rewrite of iTOL
• HTML5 Canvas based display engine
• Many new bugs introduced (probably :-)
• Too many changes to list...

Version 2.9

• New database based backend tree storage system
• Additional tree can be displayed above the heatmap datasets
• Support for display of custom scales in several dataset types
• Various minor updates and bug fixes

Version 2.2.2

• Collapsed clades can be exported with same size and font as regular leaves

Version 2.2.1

• Colored strip and gradient datasets support values assigned to internal tree nodes. These values will only be displayed when assocated clades are collapsed.
• Collapsed clades can be displayed with simplylified triangles, taking less space

Version 2.2

• multiple binary datasets will be automatically spread to prevent overlap
• If labels are present in a color strip dataset, a legend containing the labels will be added to exported trees

Version 2.1.1

• branches can be marked with custom labels
• Dataset labels are optional in exported trees

Version 2.1

• New dataset type: circles
• Several datasets (binary, bar chart, multi-value bar chart, protein domains) support display of values associated with internal nodes of the tree. These values will only be displayed when assocated clades are collapsed.

Version 2.0.1

• Pie chart position on each branch can be defined: example

Version 2.0

• New dataset type: connections

Version 1.9

• custom information can be displayed in node popups; basic HTML and CSS are supported, with links and images

Version 1.8.3

• trees can be rerooted when exported through batch access

Version 1.8.2

• name based node filtering in the automatic NCBI tree generator

Version 1.8.1

• protein IDs/ACCs (Uniprot and NCBI) supported in the automatic NCBI tree generator

Version 1.8

• new tree display mode: unrooted
• branches can be automatically colored based on bootstrap values

Version 1.7.1

• text label colors can be defined

Version 1.7

• new dataset type: boxplot
• individual fileds in multi-value barchart datasets can be automatically aligned
• PhyloXML tree format supported for upload and export
• Automatic NCBI tree generator expanded with support for scientific names and subtrees

Version 1.6.1

• color ranges and clade colors can be defined during upload
• heatmap legends displayed
• option to prevent overlap of color strips and gradients with other datasets

Version 1.6

• Batch access through a simple API. Both tree upload and export are supported.

Version 1.5

• new dataset type: heatmaps

Version 1.4.1

• leaf labels can be aligned in both modes
• color ranges expandable to whole clades
• maximum bar and protein size increased to 5000 pixels

Version 1.4

• mid-point rooting function

Version 1.3.2

• protein domain datasets are now auto scaled; protein size is not limited
• 5 new domain shapes available

Version 1.3.1

• collapsed clades can be defined during upload

Version 1.3

• Shared projects

Version 1.2.1

• auto remove branches with low bootstrap support
• optimal font size calculation during export

Version 1.2

• new dataset types: protein domain architectures and time-series
• search results dynamically highlighted in the tree
• major restructuring and code cleanup, resulting in significant speed improvements

Version 1.1.1

• improved interactive tree coloring tool, with branch coloring
• import and export of trees in NEXUS format

Version 1.1

• branch coloring through the 'color strips' dataset
• personal accounts
• keyboard navigation and mousewheel zooming
• improved tree search
• pie-charts can be displayed together with another dataset
• bug fixes

Version 1.03

• inverted circular display mode
• streamlined and simplified display page header
• font size and branch width can be changed during export

Version 1.02

• new dataset type: internal node pie-charts
• Leaf labels can be styled on the exported trees (bold, italic or bold-italic)
• auto-collapsing of clades based on average branch lenghts
• various small bug fixes

Version 1.01

• new dataset types: color gradients and colored strips
• labels for internal nodes can be uploaded
• branch lengths can be displayed directly on the tree
• various small bug fixes

Version 0.99

initial release