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phylorug: Visualize Clade Recovery and Support Across Phylogenetic Trees

Source: R/phylorug-package.R
phylorug-package.Rd

Generates rug plot visualizations directly on tree nodes to illustrate clade recovery and support from multiple phylogenetic and phylogenomic analyses. See vignette("phylorug") for a detailed guide.

Core functions

read_trees

Read tree files from disk

translate_tips

Rename specimen codes to species names

check_taxa

Diagnose taxon consistency across trees

prune_to_shared

Prune trees to shared taxa

node_presence_matrix

Build the presence/support matrix

plot_phylorug

Draw the rug plot on a reference tree

add_tree

Add a tree to an existing matrix

References

Wheeler, W.C. (1995). Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Systematic Biology, 44(3), 321-331. doi:10.1093/sysbio/44.3.321

Giribet, G. (2003). Stability in phylogenetic formulations and its relationship to nodal support. Systematic Biology, 52(4), 554-564. doi:10.1080/10635150390223730

Sanders, J.G. (2010). Program note: Cladescan, a program for automated phylogenetic sensitivity analysis. Cladistics, 26(1), 114-116. doi:10.1111/j.1096-0031.2009.00280.x

Machado, D.J. (2015). YBYRA facilitates comparison of large phylogenetic trees. BMC Bioinformatics, 16, 204. doi:10.1186/s12859-015-0642-9

Wolfe, J.M. et al. (2019). A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans. Proceedings of the Royal Society B, 286(1901), 20190079. doi:10.1098/rspb.2019.0079

Fu, Y. et al. (2025). Phylogenomic insights into the higher level relationships within Culicomorpha (Diptera). Insect Systematics and Diversity, 9(6), ixaf056. doi:10.1093/isd/ixaf056

Montanaro, G., Lopes, F. et al. (2026). Phylogenomics resolves a 200-year-old puzzle: a revised tribal classification of Afro-Eurasian dung beetles (Coleoptera: Scarabaeinae). bioRxiv. doi:10.64898/2026.07.22.740134

See also

Useful links:

Author

Maintainer: Md Rifath Ahamed rifathahamed777@gmail.com (ORCID) [copyright holder]

Authors: