07. FAQ

Troubleshooting and FAQ

I double-clicked a .newick file and nothing happened (or the wrong app opened).

On macOS, the file associations are set up by the .pkg installer; if you copied an .app bundle by hand, the OS may not have registered the document types yet. Try opening any .newick file by right-clicking it and choosing Open With → TreeHouse, or open it from inside TreeHouse via File → Open File. On Windows, use File → Register File Associations (visible in debug builds) or right-click a tree file and choose Open with → Choose another app → TreeHouse.

“Could not parse file data as text” / “Could not read file.”

The file either is not valid UTF-8 text or could not be read from disk. Make sure the file is a plain-text Newick or Nexus file (not a binary phylogeny format), and that you have read permission for it.

The tree opened but it is blank / has no labels.

Check the Tip Labels, Internal Labels, and Branch Lengths toggles in the left side bar. All three options are independent and one may be turned off. Increase the corresponding font size slider if the labels are too small to see at the current zoom level.

I cannot toggle the Plot pane.

The Plot pane is only enabled when (a) the tree has branch lengths, and (b) the Distance Unit is set to anything other than Unitless. If your tree has no branch lengths, there is nothing meaningful to plot.

The Geological Time Scale toggle is greyed out.

GTS is only meaningful when the Distance Unit is Million years. Switch the unit and the toggle will become available.

My very large tree is slow to draw or scroll.

TreeHouse is designed for fast rendering, but extremely large trees (hundreds of thousands of tips) are still demanding. Try switching from Phylogram to Fan style for a more compact overview, turning off Tip Labels, reducing the Edge Spacing / Width sliders, or using View Subtree to focus on a clade of interest.

I re-rooted the tree but want to undo the change.

There is currently no in-app undo history. To return to the original tree, re-open the file with File → Open File.

Saving as Nexus produced an empty file.

Nexus writing is not yet implemented; only Nexus reading is supported. Save to Newick instead.

How do I report a bug or request a feature?

Please create an issue on the GitHub repository: https://github.com/karolisr/treehouse/issues. Include your operating system, the TreeHouse version (visible in App → About on macOS, or in the Cargo.toml of the source you built from), and an example tree file that reproduces the problem.