The desktop viewer for figures worth publishing.
A mature, offline phylogenetic tree viewer built for publication-quality figures — with integrated taxonomy and sequence annotation, protein-domain architectures, and time axes that reach from calendar dates back through deep geologic time.
Self-contained installers with a bundled runtime — no Java to install. All releases ↗
Every rival has some of these. None brings them together on a mature, offline desktop — where a figure is finished the moment you export it.
Pull UniProt / NCBI taxonomy, sequence data, and protein-domain architectures straight onto the tree — no side pipeline, no hand-drawn overlays.
Tip-dated calendar axes for molecular epidemiology, and a full ICS geologic time scale for the fossil record — the deep-time figure no other viewer draws.
WYSIWYG PDF, SVG, and EPS from the same renderer that draws the screen — outline text, figure-grade by construction, ready for Illustrator or a manuscript.
Every edit is undoable, and every tree-changing operation records what it did — so a figure stays reproducible and a mistake is never one click from permanent.
Thousands of tips stay responsive across rectangular, circular, and unrooted views — with tip-aligned annotation columns that ride into circular rings.
Newick, NHX, Nexus, phyloXML — plus Nextstrain / Auspice JSON, tip-dated labels, and BEAST intervals. Open the file you have; get a figure.
Every image on this page was rendered by the program from a bundled example tree, exported without editing. Load the same trees from File → Demo Trees.
Categorical strips and a numeric heat ring wrap the tree — the annotation-column figure, drawn as rings.
Reconstructed geographic states as per-node pies, straight from a Nextstrain-style dataset.
Per-tip domain diagrams aligned beside the tree — the functional-genomics view, built in.
Color tips and clades by any column — categorical palettes or continuous gradients, with a movable key.
Give Archaeopteryx a tree of named taxa and it resolves each lineage against NCBI — then colorizes every clade by any rank in a single click, entirely offline when the ranks travel in the file.
Download the installer for your OS and open it. The runtime is bundled — there's no Java to set up.
Drop in your Newick / phyloXML / Nexus / Auspice JSON, or start from File → Demo Trees to see a feature at work.
Style it, then File → Export to PDF, SVG, or EPS. What you see is exactly what you get.
Archaeopteryx is the interactive front of forester — an open-source Java library and a suite of command-line tools for phylogenetics. Explore and finish a figure by hand here; batch or script the same operations headlessly for reproducible, regenerate-from-config pipelines.
A dedicated publication is in preparation. Until it appears, please cite the software directly — the repository's Cite this repository button provides a ready-made reference, and each release is archived with a citable DOI.
Christian M. Zmasek · Archaeopteryx · https://github.com/cmzmasek/archaeopteryx
Archaeopteryx