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bioRxiv · 10.64898/2026.08.27.747475

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

Zeng, Z.·Wang, Y.
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Abstract

FigTree is a long-standing phylogenetic tree viewer, but its GUI-centered workflow does not itself provide a versioned, batch-replayable record of styling operations. We present FigTreeKit, a Python package that serializes a supported subset of FigTree 1.4.4 annotations (!hilight, !color, and !font), audits taxonomy mappings before topology-gated clade collapse, retains selected BEAST-style metadata in the tested fixtures, and invokes a patched FigTree renderer for headless PNG, PDF, and SVG output. Across 60 independently generated balanced trees with 50-10,000 taxa (10 trees per size, each timed 10 times as technical replicates), the tree-level log-log slope of export time was 0.96 (95% confidence interval [CI], 0.91-1.01), which is compatible with approximately linear scaling over the tested range but does not prove it. The 189,801-taxon GTDB R232 bacterial reference tree was parsed and exported as a large-data scalability demonstration. On the 10,122-taxon GTDB R232 archaeal reference tree, the scripted workflow assessed 179 order-level groups; 142 multi-tip groups produced non-trivial collapses, whereas 37 singleton groups did not alter the display. The software is accompanied by 796 passing tests, a golden conformance corpus that includes acceptance tests against the bundled FigTree JAR, deterministic scenario-based topology checks, and an overall statement coverage of 81%, reported as a descriptive engineering metric. FigTreeKit is released under the GPL-2.0-or-later license as the figtreekit package on PyPI, with source code, documentation, and benchmark data archived on Zenodo.

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Zeng, Z., Wang, Y.. 2026-08-28. FigTreeKit: A Python toolkit for programmatic FigTree styling, taxonomy-aware clade auditing, and phylogenetic tree rendering. https://doi.org/10.64898/2026.08.27.747475

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