Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

Provides a single-function pipeline for automated collapsing and visualization of large phylogenetic trees with geological timescales. Automatically parses taxonomic labels from multiple formats (GTDB, Silva, NCBI, embedded, custom), identifies Most Recent Common Ancestors (MRCAs), assigns color-blind-safe palettes, executes batch collapsing with automatic nesting-aware ordering, integrates 'deeptime' geologic time scales with adaptive time breaks and unit switching, and manages smart legend layout. Supports special ancestral node identifiers (LUCA, LACA, LBCA) for highlighting key nodes in the tree of life. Provides external taxonomy file support for trees with incomplete or missing taxonomic labels. Features real-time logging with timestamps, step tracking, and multiple log levels. Includes comprehensive input validation for tree and sequence file formats. Reduces a 60-line manual workflow to a single function call while preserving full compatibility with the 'ggtree'/'deeptime' ecosystem. The visualization pipeline builds on 'ggtree' Yu et al. (2017) <doi:10.1111/2041-210X.12628>, 'deeptime' Gearty (2025) <doi:10.1080/20964471.2025.2537516>, and 'ape' Paradis and Schliep (2019) <doi:10.1093/bioinformatics/bty633>.

install.packages("Rclade")

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