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Version 2.2.0

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@arklumpus arklumpus released this 26 Oct 13:53
· 14 commits to main since this release
v2.2.0
d858f0a

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.

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.

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!

Assets 10