How to uninstall Jalview on Mac
Before removing Jalview, save and copy your alignment files and Jalview projects to a separate backup, then open the copy. This guide covers the official Mac download; Homebrew-specific removal is separate below.
Quit and remove the app
Finish current work and quit Jalview. Check Activity Monitor for its process before removing the app in Finder. In Applications, move Jalview.app to the Trash; if you keep it elsewhere, use its actual location. Keep the Trash until your backup has been checked. Official documentation
Review local data
These exact locations were observed in the removal record. Open them through Finder’s Go › Go to Folder. Copy wanted contents first; leave them if you want to keep settings or cannot establish ownership. They are optional data removal, not a prerequisite for removing the app.
~/.jalview_properties~/.jalview.log~/Library/Application Support/Jalview-Desktop
Check the result
This read-only check searches full process command lines, not disk contents.
pgrep -ifl 'Jalview'
No output with exit status 1 means no matching command line was found. A printed entry needs inspection in Activity Monitor because names can match unrelated processes. An error is not proof of removal. Also check that the app is absent from its original Finder location; a retained data folder or independent component does not mean the app is still installed.
If you installed it with Homebrew
Use the installed cask receipt and uninstall without zap.
brew uninstall --cask jalview
It also removes the managed jalview command link. The live cask additionally names these zap targets, which can erase settings, local data or integration files; this is Homebrew’s list, not a vendor data-location claim.
~/.jalview_properties~/Library/Saved Application State/org.jalview.jalview-desktop.savedState
A direct brew uninstall --cask --zap jalview runs its own zap scope without consulting Mole’s checkboxes. Mole uses zap only when the complete scope passes its gate; unchecked or shared paths, paths outside the review boundary, unknown stanzas and unsupported directives suppress it. Selected remnants still use Mole’s deletion path.
What Mole lists
~/.jalview_properties is listed for review and is not selected by default. ~/.jalview.log is listed for review and is not selected by default. ~/Library/Application Support/Jalview-Desktop is listed for review and is not selected by default.
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.
What this test covered
The September 21, 2026 record covers the following test. The official download ran and was removed. The two hidden home files survived that removal and were subsequently added as reviewed leaves; their collection was not verified in that original test.