FigTree is a free, open-source desktop application for macOS (and other platforms) that renders and annotates evolutionary trees produced by Bayesian and maximum-likelihood phylogenetic analysis software.
What is FigTree?
FigTree is a graphical viewer for phylogenetic trees, purpose-built to work alongside BEAST and MrBayes output but equally at home with any standard Newick or NEXUS file. It was created by Andrew Rambaut at the University of Edinburgh and has become a quiet staple of computational biology labs worldwide — the tool you open the moment your MCMC run finishes and you want to actually see what the data is telling you.
I've spent weeks loading posterior tree samples into it, colouring clades by posterior probability, and exporting publication-ready SVGs, and I keep coming back to one quality: it stays out of your way. There are no subscription prompts, no cloud sync, no telemetry. It reads your tree file, draws it, and lets you think.
What does FigTree do best?
FigTree excels at annotating trees with metadata — node labels, branch colours, tip shapes — without requiring you to write a single line of code. You can pull in annotation columns from a TSV, map them to visual properties via the Appearance panel, and produce a fully annotated cladogram in minutes.
- Flexible layouts: rectangular, polar, radial, and unrooted layouts; all switchable at runtime.
- Annotation-driven styling: colour branches by any numeric or categorical annotation; gradient colouring for continuous traits like divergence dates.
- Node statistics: posterior probabilities and bootstrap values surface cleanly as node labels or scaled circles.
- Time-scaled trees: when your BEAST output carries date annotations, FigTree renders a proper timescale axis — indispensable for viral phylodynamics work.
- Export options: PDF, SVG, PNG, and EPS make it straightforward to drop a figure directly into a manuscript.
The annotation panel is where FigTree earns its reputation. Once you've mapped a tip-attribute file to visual properties, you can toggle layers on and off to tell a story visually — something R's ape or ggtree can do too, but with far more typing.
Is FigTree free?
Yes — FigTree is completely free and open-source, licensed under the GNU Lesser General Public License. There is no paid tier, no premium feature set, and no registration required. The source lives on GitHub and can be compiled from scratch, or you can grab the pre-built macOS JAR from the releases page. Because it runs on the Java Virtual Machine, it works on Apple Silicon Macs with any reasonably modern JDK installed.
Who should use FigTree?
FigTree is written for researchers and graduate students in evolutionary biology, epidemiology, and population genetics who are already producing phylogenetic trees and need a reliable way to visualise and present them. If you're running BEAST analyses on SARS-CoV-2 sequences, tracing influenza migration patterns, or reconstructing mammalian divergence times, FigTree belongs in your toolkit.
It is not a tree-building application — it doesn't run alignment or inference. For that you'll want IQ-TREE, RAxML, or BEAST itself. FigTree is strictly downstream: the presentation layer after the heavy computation is done.
Compared to alternatives like Dendroscope (which handles enormous trees with millions of tips more gracefully) or iTOL (a web-based viewer with slick circular layouts and sharing features), FigTree occupies a comfortable middle ground: richer annotation control than most quick-and-dirty tools, but without the steep learning curve of scripting trees in R's ggtree package.
What are the best FigTree alternatives?
The closest desktop competitors are Dendroscope (better for massive trees, free, Java-based) and TreeAnnotator (BEAST's own summarising companion, not a viewer per se). Online, iTOL (Interactive Tree of Life) offers gorgeous circular layouts and one-click sharing but requires an account for private trees. For programmers, ggtree in R gives you complete programmatic control at the cost of a steep ggplot2 learning curve. FigTree wins when you want point-and-click annotation fidelity without leaving the desktop.
How actively maintained is FigTree?
FigTree is mature, stable software rather than rapidly iterating. The core feature set has been solid for years, and while major releases are infrequent, the GitHub repository remains open and issues are monitored. For a tool at this stage of scientific software life, stability is a feature — you don't want your visualisation layer changing behaviour between paper revisions. That said, if you hit a Java compatibility snag on a newer macOS release, check the GitHub issues page first; the community usually has a workaround within days.
