How to uninstall TreeViewer on Mac

TreeViewer is a modular desktop visualization tool for phylogenetic trees and evolutionary biology datasets. Phylogenetic tree files and datasets you opened in TreeViewer stay where you saved them; removing the app does not delete those research files. However, TreeViewer downloads optional analysis module packages into ~/.local/share/TreeViewer. Because this directory sits directly under your home folder outside ~/Library, copy ~/.local/share/TreeViewer first if you installed modular extensions and want to preserve them. This guide covers the official Mac app and Homebrew cask treeviewer.

Quit and remove the app

  1. Press Command + Q inside TreeViewer, or choose TreeViewer › Quit TreeViewer. If a welcome prompt offers to download module extensions, decline it unless you intend to install them.
  2. Open Finder, navigate to Applications, and drag TreeViewer.app to the Trash.

Review local data

These paths are declared in the Homebrew cask and were inspected during the recorded test. In Finder, press Shift + Command + G for the Library path. The share folder is located under your user home directory inside .local/share.

Location What it holds What to do
~/.local/share/TreeViewer Installed analysis modules, plugins, and settings Settings and any modules you installed. Copy it first. A direct Homebrew zap removes it. Mole lists it and leaves it unselected, including when Remove data and settings with apps is on, because this path is outside ~/Library. Select it only after you have a copy.
~/Library/Saved Application State/io.github.arklumpus.TreeViewer.savedState Saved window restoration state Saved window state. Mole selects this folder when it is present.

Check the result

pgrep -il TreeViewer
ls -ld "/Applications/TreeViewer.app" "$HOME/.local/share/TreeViewer" "$HOME/Library/Saved Application State/io.github.arklumpus.TreeViewer.savedState"
  • No output from pgrep means no TreeViewer process is running.
  • A printed line from pgrep indicates an active process. Inspect it in Activity Monitor before continuing.
  • An error from pgrep does not prove the app has quit.
  • A path printed by ls is still present on disk.
  • No such file or directory confirms that path has been completely removed.
  • Permission denied means your account lacks read access for that directory. Check your tree files separately.

If you installed it with Homebrew

brew uninstall --cask treeviewer

The cask zap list includes ~/.local/share/TreeViewer and ~/Library/Saved Application State/io.github.arklumpus.TreeViewer.savedState. Running brew uninstall --cask --zap treeviewer removes that list unconditionally and does not read Mole's checkboxes. Copy ~/.local/share/TreeViewer first if you installed modules. Mole checks the full removal list and skips --zap when it reaches unchecked data, shared files, or a path it cannot verify. Leftovers you selected still use Mole's own removal.

What Mole lists

Mole lists ~/.local/share/TreeViewer and leaves it unselected. Turning on Remove data and settings with apps in General › Cleaning does not select this folder. Mole selects ~/Library/Saved Application State/io.github.arklumpus.TreeViewer.savedState when that folder is present. Tree files outside ~/.local/share/TreeViewer are not part of this list.

These defaults assume “Remove data and settings with apps” is off. Opting in also selects eligible reviewed app data; shared stores and protected data retain individual review or stay locked. ~/.local/share/TreeViewer stays unselected either way.

What this test covered

On October 9, 2026, TreeViewer 2.2.0 from the official arm64 package was copied into Applications. The welcome window was set to skip module installation and then cancelled. No modules were downloaded. The recorded removal included the app and ~/.local/share/TreeViewer after that folder was selected. The saved-state folder was not present. Status showed one TreeViewer row while it was running. No new launch agent was found. Mole's update page was not opened. A Homebrew install was not tested.