04. Exporting

Saving and Exporting

TreeHouse provides three ways to save your work:

Action	Second Header
Save As… (Newick)	Choose File → Save As… (or Cmd+S / Ctrl+S). A standard file dialog lets you save the currently displayed tree as a Newick file (.newick or .tre). The window title updates to the new filename. Trees are written including any modifications you have made during the session (re-rooting, removed nodes, etc.).
Save Current Subtree	When a subtree view is active, File → Save Current Subtree (or Cmd+E / Ctrl+E) saves only the visible subtree as a new Newick file, leaving your in-memory tree untouched.
Export as PDF	File → Export as PDF (or Cmd+P / Ctrl+P) renders the current view to a high-quality, vector PDF using oxidize-pdf. The PDF reflects whatever is on the canvas at the time of export (i.e. style (phylogram or fan), label visibility, scale bar, clade highlights, and so on) so use the side-bar options to set up the figure exactly as you want it before exporting.

Note

As of this manual's writing, saving directly to Nexus is not yet implemented. The menu accepts the extension, but the file will not be written. If you need a Nexus output, save to Newick first and convert externally. PDF export and Newick saving are fully supported.