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Author

Zi-Chao Zeng

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Open access Aug 2026

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

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 ma...

Zi-Chao Zeng, Yin-Zhao Wang · 0 citations
Open access Sep 2026

Rclade: automated taxonomic collapsing and geological-timescale annotation of time-calibrated phylogenetic trees in R

Background Reproducible taxonomic collapsing and geological-timescale annotation of time-calibrated phylogenetic trees in R often require coordination among several packages and repeated code for label parsing, clade validation, plotting, and export. Workflow-managed analyses additionally benefit from non-interactive c...

Zi-Chao Zeng, Yin-Zhao Wang · 0 citations
Open access Aug 2026

PyiTOL: reproducible Python workflows for iTOL annotation and taxonomic monophyly assessment

PyiTOL validates inputs, generates 31 iTOL template schemas, performs LCA-based monophyly classification with nested-monophyly detection, sampling-completeness states and polyphyletic subgroup decomposition, plus API upload and session replay.

Zi-Chao Zeng, Yin-Zhao Wang · 0 citations

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