PyiTOL: reproducible Python workflows for iTOL annotation and taxonomic monophyly assessment
TL;DR
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.
Abstract
Motivation The Interactive Tree of Life (iTOL) is widely used to display and annotate phylogenetic trees, but managing its format-sensitive annotation files impede reproducible high-throughput analyses. Among the maintained Python packages and versions evaluated, none combined template generation, taxonomic monophyly assessment and iTOL batch operations. Results PyiTOL validates inputs, generates 31 iTOL template schemas (22 accepted by the live batch uploader), performs LCA-based monophyly classification with nested-monophyly detection, sampling-completeness states and polyphyletic subgroup decomposition, plus API upload and session replay. On a topology-constructed benchmark, all calls matched prespecified labels for 4,389 groups; on a 700-genome tree, binary mono/non-mono calls agreed with ETE4 for 409 genera; 17,294 GTDB R232 genera were processed in about 17 s. Availability and Implementation PyiTOL 1.0.3 (Python ≥3.10; Linux, macOS and Windows) is MIT-licensed at https://github.com/ZengZichao/PyiTOL and archived with test data at Zenodo (https://doi.org/10.5281/zenodo.22106806). Contact wyz@sjtu.edu.cn