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)
Automated Deep-Time Phylogenetic Tree Collapsing and Visualization
Version: 1.1.5
Rclade provides a single-function pipeline for automated collapsing and visualization of large phylogenetic trees with geological timescales.
The GitHub repository is at https://github.com/zengzichao/Rclade. Report issues at https://github.com/zengzichao/Rclade/issues.
From the fixed GitHub release tag (requires the remotes package):
remotes::install_github("zengzichao/[email protected]")
Or from a downloaded release tarball (GitHub Releases / Zenodo archive):
install.packages("Rclade_1.1.5.tar.gz", repos = NULL, type = "source")
library(Rclade)
data(example_tree)
p <- plot_timetree(example_tree, rank = "phylum", add_timescale = FALSE)
print(p)
Zeng Z (2026). Rclade: automated taxonomic collapsing and geological-timescale annotation of time-calibrated phylogenetic trees in R. bioRxiv. doi:10.64898/2026.08.27.747462
MIT + file LICENSE