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Rclade

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.

• English README
• 中文 README
• Online documentation (pkgdown): https://zengzichao.github.io/Rclade/

The GitHub repository is at https://github.com/zengzichao/Rclade. Report issues at https://github.com/zengzichao/Rclade/issues.

Installation from source

From the fixed GitHub release tag (requires the remotes package):

remotes::install_github("zengzichao/Rclade@v1.1.5")

Or from a downloaded release tarball (GitHub Releases / Zenodo archive):

install.packages("Rclade_1.1.5.tar.gz", repos = NULL, type = "source")

Quick start

library(Rclade)
data(example_tree)
p <- plot_timetree(example_tree, rank = "phylum", add_timescale = FALSE)
print(p)

Reference

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

License

MIT + file LICENSE

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.