FigTreeKit: A Python toolkit for programmatic FigTree styling, taxonomy-aware clade auditing, and phylogenetic tree rendering

FigTree is a widely-used phylogenetic tree viewer, but its graphical user interface workflow lacks a versioned, batch-replayable record of styling operations. FigTreeKit, a Python package, addresses this limitation by serializing a subset of FigTree 1.4.4 annotations, auditing taxonomy mappings, and retaining BEAST-style metadata. It also invokes a patched FigTree renderer for generating headless PNG, PDF, and SVG outputs.

In a test involving 60 independently generated balanced trees with 50-10,000 taxa, the tree-level log-log slope of export time was found to be 0.96 (95% CI, 0.91-1.01), suggesting approximately linear scaling over the tested range. The software was able to parse and export the 189,801-taxon GTDB R232 bacterial reference tree, demonstrating its large-data scalability.

The FigTreeKit workflow assessed 179 order-level groups on the 10,122-taxon GTDB R232 archaeal reference tree, with 142 multi-tip groups producing non-trivial collapses and 37 singleton groups not altering the display. The software is backed by 796 passing tests, a golden conformance corpus, and an overall statement coverage of 81%, making it a reliable and robust tool for phylogenetic tree styling and analysis.

FigTreeKit is available under the GPL-2.0-or-later license on PyPI, with source code, documentation, and benchmark data archived on Zenodo.