Version 2.2.0

Update instructions

If you installed TreeViewer using the installer (from a `.msi`, `.pkg` or `.run` file)

Just download the latest version of the installer and run it as normal. It will take care of removing any incompatible modules/settings, but will preserve your preferences where possible.

• For Windows: download TreeViewer-Win-x64.msi
• For macOS on Apple Silicon (ARM) processors: download TreeViewer-Mac-arm64.pkg
• For macOS on Intel (x64) processors: download TreeViewer-Mac-x64.pkg
• For Linux: download TreeViewer-Linux-x64.run

If you installed TreeViewer manually (from a `.zip`, `.dmg` or `.tar.gz` file)

• On Windows:
  Download the latest archive file, and extract it somewhere (e.g. delete the files in the old TreeViewer folder and replace it with the new files). Then, open a command line in the folder where you have extracted the files and run the following command:

  .\TreeViewer --welcome
  

  This will clear the module cache and open the "Welcome window" from which you can install the new modules.

• On macOS:
  Download the latest disk image, double-click it to mount it, and drag TreeViewer into your Applications folder. Then, open a command line and run the following command:

  rm -r ~/.local/share/TreeViewer/modules*
  

  This will clear the module cache. If you now open TreeViewer, it will show you the "Welcome window" from which you can install the new modules.

• On Linux:
  Download the latest archive file, and extract it somewhere (e.g. delete the files in the old TreeViewer folder and replace it with the new files).
  Then, open a command line in the folder where you have extracted the files and run the following command:

  chmod +x TreeViewer TreeViewerCommandLine DebuggerClient
  ./TreeViewer --welcome

  This will clear the module cache and open the "Welcome window" from which you can install the new modules.

Note that you cannot use two different versions of TreeViewer at the same time.

• For Windows: download TreeViewer-Win-x64.zip
• For macOS on Apple Silicon (ARM) processors: download TreeViewer-Mac-arm64.dmg
• For macOS on Intel (x64) processors: download TreeViewer-Mac-x64.dmg
• For Linux: download TreeViewer-Linux-x64.tar.gz

See Installing TreeViewer for more instructions on how to install TreeViewer, including information on how to install the program on a headless server without admin privileges.

New features

• There is a new "Spreadsheet" editor function that can be used to more easily edit attachment tables.
• When drawing an alignment together with the tree, there is now an option to automatically position the sequences at the tip nodes, in addition to having a single "alignment block".
• Branch reference settings have been removed in response to comments from reviewers. All Plot action modules now automatically detect the Coordinates module that is being used, and use that information to determine the shapes of the branches.
• The Prune node module now has the option to keep only the selected node(s), rather than pruning it/them (i.e., to prune everything else).
• The Replace attribute module now supports using regexes to replace strings with numbers.
• There is a new command-line option to install all modules (-I). This is useful for headless installs.
• The gradient editor window now shows gradient units relative to the specified maximum and minimum (instead of 0 to 1).
• Coordinate modules now have "Coordinate shift" options that can be used to manually change the position of some nodes.
• Action modules (e.g., Custom action script and Spreadsheet editor) can now be active even when no tree has been loaded.

New modules

• A new module to change the tree topology by pruning and regrafting a subtree.
• A new module to open a spreadsheet editor.

Bugfixes

• An invalid regex in the search box now causes a warning to be displayed, instead of crashing the program.
• Tree files in Newick format that have spaces in the tip names and where the tip names are not quoted should now work correctly (#16).
• Prevent an error in the Replace attribute module when the replacement value is null.
• Prevent a crash when an invalid sequence alignment attachment is selected.
• Prevent a crash when using the GTR model to compute distances between sequences that are too divergent.
• Fixed an issue with the appearance of dashed lines in images exported as PNG or TIFF.
• Fixed issues with the csc command-line command.
• Attribute names are now trimmed in formatter windows (e.g., Support is equivalent to Support).
• The colours used by the Auto colour by node options (and variants) are now consistent when running the program multiple times.
• Fixed boundary determination for the Node bars module.
• Trees drawn in circular style now have a minimum size.
• Fixed some issues when applying the tree style to another tree file.
• Fixed an issue that caused modal dialogs to flash on macOS when multiple dialogs are shown on the same window (e.g., when opening a file containing untrusted source code).

Let me know if you have any problems in the Issues section!

Version 2.1.0

Important note for macOS users on Apple silicon (ARM) processors: if you allow TreeViewer to update itself, it will attempt to update using the Intel (x64) package, which will complain about being incompatible with your computer. Please manually download the TreeViewer-Mac-arm64.pkg setup package to install the new version instead!

Update instructions

If you installed TreeViewer using the installer (from a `.msi`, `.pkg` or `.run` file)

Just download the latest version of the installer and run it as normal. It will take care of removing any incompatible modules/settings, but will preserve your preferences where possible.

• For Windows: download TreeViewer-Win-x64.msi
• For macOS on Apple Silicon (ARM) processors: download TreeViewer-Mac-arm64.pkg
• For macOS on Intel (x64) processors: download TreeViewer-Mac-x64.pkg
• For Linux: download TreeViewer-Linux-x64.run

If you installed TreeViewer manually (from a `.zip`, `.dmg` or `.tar.gz` file)

• On Windows:
  Download the latest archive file, and extract it somewhere (e.g. delete the files in the old TreeViewer folder and replace it with the new files). Then, open a command line in the folder where you have extracted the files and run the following command:

  .\TreeViewer --welcome
  

  This will clear the module cache and open the "Welcome window" from which you can install the new modules.

• On macOS:
  Download the latest disk image, double-click it to mount it, and drag TreeViewer into your Applications folder. Then, open a command line and run the following command:

  rm -r ~/.local/share/TreeViewer/modules*
  

  This will clear the module cache. If you now open TreeViewer, it will show you the "Welcome window" from which you can install the new modules.

• On Linux:
  Download the latest archive file, and extract it somewhere (e.g. delete the files in the old TreeViewer folder and replace it with the new files).
  Then, open a command line in the folder where you have extracted the files and run the following command:

  chmod +x TreeViewer TreeViewerCommandLine DebuggerClient
  ./TreeViewer --welcome

  This will clear the module cache and open the "Welcome window" from which you can install the new modules.

Note that you cannot use two different versions of TreeViewer at the same time.

• For Windows: download TreeViewer-Win-x64.zip
• For macOS on Apple Silicon (ARM) processors: download TreeViewer-Mac-arm64.dmg
• For macOS on Intel (x64) processors: download TreeViewer-Mac-x64.dmg
• For Linux: download TreeViewer-Linux-x64.tar.gz

See Installing TreeViewer for more instructions on how to install TreeViewer.

New features:

• Added new buttons to redraw all plot elements and to reset the parameters of the Coordinates module to the default values.
• Added Undo/Redo functionality (#10).
• Added Stats window to compute tree statistics (with a tutorial in the wiki).
• The Search function now uses a different colour to highlight nodes and can move the plot view to focus on the matched nodes. When a single node is matched (with the Find next or Find previous buttons), that node is selected; when multiple nodes are matched (with the Find all button), they are highlighted without being selected.
• Modules can now issue "warnings" if they think something is wrong (e.g., you are drawing the root branch on an unrooted tree).
• Plot errors and warnings cause an icon to appear in the status bar. The icon can be clicked to open a window listing all the errors/warning; clicking an error or warning in this window highlights the module that caused it in the main window.
• Plots can now be exported in TIFF format, as well as PDF, SVG and PNG (both in the UI and in command-line mode).
• When "copying" the modules from one tree to another, there is now the option to choose which modules are copied, as well as to apply the modules to a tree that is currently opened in another window.
• The program icons should now fit more with the look of modern OSs.
• TreeViewerCommandLine now has a csc command to compile and execute C# scripts.
• Added a new text conversion option (which is the new default) when exporting SVG files, which greatly reduces the output file size.
• Plot action modules now attempt to detect the current coordinate modules and set the branch reference appropriately.
• The Set up age distributions (attachment) module now supports MCMCtree-style tables of age distributions.
• Multiple age distributions can now be drawn on the same tree (see tutorial in the wiki).
• Modules that set up age distributions now have an option for scaling the age distribution and the tree.

New modules

• A new module to create random trees and (constrained) Neighbour-Joining/UPGMA trees from sequence alignments or distance matrices.
• A few new modules to create and deal with "crop regions" that can be used to export only part of the plot (#11 and tutorial in the wiki), both in the UI and in command-line mode.
• A new Custom action script module that can be used to execute C# code from the main window.
• A new File type module to open RevBayes tree trace files.
• New module to compare one tree with another tree or with multiple other trees (with a tutorial in the wiki).
• New module to subsample trees.
• New module to parse age distributions (e.g., fossil calibrations) from an attribute on the tree (see tutorial in the wiki).

New tutorials

• New tutorial to plot multiple age distributions on the same tree.
• New tutorial to plot the results of a stochastic mapping analysis.
• New tutorial showing how the options to create new trees in TreeViewer work.
• New tutorial showing how to create and export "crop regions".
• New tutorial to compute and interpret tree statistics.
• New tutorial to perform tree comparisons

Bugfixes:

• Fixed a few bugs occurring when exporting modules including external references.
• Prevent a crash occurring sometimes when using a keyboard shortcut for a selection action.
• Fixed an issue occurring when resizing the selection panel.
• Fixed a bug causing some parameters for duplicated modules to be linked to each other.
• Fixed a bug that caused Use selection buttons to be disabled when modules are reordered.
• Fixed some issues with tooltip lingering for longer than they were expected to.
• Fixed a bug with midpoint rooting.
• Fixed some issues with fonts not being exported in PDF files.
• Guid-like attributes (e.g., age distributions) are now preserved when pruning nodes close to the root node.
• Fixed some issues with the Scale axis module on circular coordinates.
• When trees are too discordant to compute a consensus tree, an error message is produced, rather than the program crashing.
• NEXUS tree files where trees are introduced by UTREE instead of TREE are now parsed correctly (#13).
• Greatly improved performance and compatibility with macOS.
  • Native build for macOS on Apple Silicon (ARM) processors.
  • TreeViewer now stays open when you close the last window, until you manually quit it (like most macOS programs).
  • Weird things no longer happen when maximising the TreeViewer window on macOS.
  • Full disk access permissions should not be necessary anymore.
  • Keyboard shortcuts should not result in the action being performed twice anymore.

Let me know if you have any problems in the Issues section!

Version 2.0.1

New features:

• --log-exceptions command-line option for TreeViewer, which logs all handled and unhandled exceptions to the standard output.

Bugfixes:

• Reading input files from the standard input on macOS and Linux now should work correctly even if the standard output is not redirected (fix for #6).
• Module IDs can again be used to select modules in TreeViewerCommandLine (regression in 2.0.0).
• The "Duplicate" buttons now look better.
• Autosaves of Markdown source code are now handled correctly.
• The colour of the title bar of the "About" window on macOS has been corrected.
• The "Stochastic map" File type module now respects the value of the "Draw simple trees after opening them" global setting.
• Dash phases are now parsed correctly in TreeViewerCommandLine
• Some modules reverted their settings to default values when opening a file (e.g. state colours for the "Node states" module); this should be fixed now.

Let me know if you have any problems in the Issues section!

Update instructions

If you installed TreeViewer using the installer (from a `.msi`, `.pkg` or `.run` file)

Just download the latest version of the installer and run it as normal. It will take care of removing any incompatible modules/settings, but will preserve your preferences where possible.

• For Windows: download TreeViewer-Win-x64.msi
• For macOS: download TreeViewer-Mac-x64.pkg
• For Linux: download TreeViewer-Linux-x64.run

If you installed TreeViewer manually (from a `.zip`, `.dmg` or `.tar.gz` file)

• On Windows:
  Download the latest archive file, and extract it somewhere (e.g. delete the files in the old TreeViewer folder and replace it with the new files). Then, open a command line in the folder where you have extracted the files and run the following command:

  .\TreeViewer --welcome
  

  This will clear the module cache and open the "Welcome window" from which you can install the new modules.

• On macOS:
  Download the latest disk image, double-click it to mount it, and drag TreeViewer into your Applications folder. Then, open a command line and run the following command:

  rm -r ~/.local/share/TreeViewer/modules*
  

  This will clear the module cache. If you now open TreeViewer, it will show you the "Welcome window" from which you can install the new modules.

• On Linux:
  Download the latest archive file, and extract it somewhere (e.g. delete the files in the old TreeViewer folder and replace it with the new files).
  Then, open a command line in the folder where you have extracted the files and run the following command:

  chmod +x TreeViewer TreeViewerCommandLine DebuggerClient
  ./TreeViewer --welcome

  This will clear the module cache and open the "Welcome window" from which you can install the new modules.

Note that you cannot use two different versions of TreeViewer at the same time.

• For Windows: download TreeViewer-Win-x64.zip
• For macOS: download TreeViewer-Mac-x64.dmg
• For Linux: download TreeViewer-Linux-x64.tar.gz

See Installing TreeViewer for more instructions on how to install TreeViewer.

Version 2.0.0

New features:

• Completely revamped interface.
• Greatly improved performance.
• Built-in examples.
• Recent files.
• New modules:
  • Reshape the tree without otherwise changing the settings of other modules.
  • Draw rectangles and text in arbitrary positions.
  • Draw branches for stochastic mapping analyses.

Bugfixes:

• On laptops, zooming using the touchpad should now work much better.
• Many more 😁

This version should be backwards-compatible with files created with the previous version of TreeViewer (i.e. you should be able to use version 2.0.0 to open any file created with TreeViewer 1.2.2 without issues, and the plot should look the same as it did under the previous version). Note however that command-line scripts that use TreeViewerCommandLine may need to be reworked a bit, because most modules have been updated (some Further transformation and Plot action modules have new parameters, while Action and Selection action modules can now have "sub-actions").

Let me know if you have any problems in the Issues section!

Update instructions

If you installed TreeViewer using the installer (from a `.msi`, `.pkg` or `.run` file)

Just download the latest version of the installer and run it as normal. It will take care of removing any incompatible modules/settings, but will preserve your preferences where possible.

• For Windows: download TreeViewer-Win-x64.msi
• For macOS: download TreeViewer-Mac-x64.pkg
• For Linux: download TreeViewer-Linux-x64.run

If you installed TreeViewer manually (from a `.zip`, `.dmg` or `.tar.gz` file)

• On Windows:
  Download the latest archive file, and extract it somewhere (e.g. delete the files in the old TreeViewer folder and replace it with the new files). Then, open a command line in the folder where you have extracted the files and run the following command:

  .\TreeViewer --welcome
  

  This will clear the module cache and open the "Welcome window" from which you can install the new modules.

• On macOS:
  Download the latest disk image, double-click it to mount it, and drag TreeViewer into your Applications folder. Then, open a command line and run the following command:

  rm -r ~/.local/share/TreeViewer/modules*
  

  This will clear the module cache. If you now open TreeViewer, it will show you the "Welcome window" from which you can install the new modules.

• On Linux:
  Download the latest archive file, and extract it somewhere (e.g. delete the files in the old TreeViewer folder and replace it with the new files).
  Then, open a command line in the folder where you have extracted the files and run the following command:

  chmod +x TreeViewer TreeViewerCommandLine DebuggerClient
  ./TreeViewer --welcome

  This will clear the module cache and open the "Welcome window" from which you can install the new modules.

Note that you cannot use two different versions of TreeViewer at the same time.

• For Windows: download TreeViewer-Win-x64.zip
• For macOS: download TreeViewer-Mac-x64.dmg
• For Linux: download TreeViewer-Linux-x64.tar.gz

See Installing TreeViewer for more instructions on how to install TreeViewer.

Version 1.2.2

Bugfixes:

• If the tree contains multiple support values (or branch lengths), they are all stored in different attributes.
• Fixed issue with attribute scroll bars in the selection panel.

New features:

• Added a button to copy an attribute from the selected tips.

Version 1.2.1

Fixes a bug with the colour picker (see also AvaloniaUI/Avalonia#6257).

Version 1.2.0

This is the first release containing fully signed (and notarized) Windows and macOS executables/installers. Also fixes some minor bugs.

Version 1.1.1

This release fixes minor bugs and adds support the NCBI ASN.1 tree format.

Version 1.1.0

This release fixes minor bugs and introduces a Markdown code editor control, as well as improving the appearance of many buttons across the interface of the program.

Version 1.0.1

This release fixes minor bugs and exposes methods used by some modules.