read_tree_auto: Read tree from file with automatic format detection

In Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

Read tree from file with automatic format detection

Description

Intended for use as a stable library API by external workflows (e.g., Snakemake/Nextflow).

Usage

read_tree_auto(filepath, tree_index = NULL, multi_tree_mode = "error")

Arguments

filepath	Path to tree file (.tre, .nwk, .newick, .nexus, .nex, .treefile, .xml)
tree_index	Integer. Index of tree to use from multiPhylo objects (e.g., BEAST posterior). Default: NULL (will use multi_tree_mode to determine behavior).
multi_tree_mode	Character. How to handle multiple trees in a file. Options: "error" (default): Stop with error and ask user to specify "ask": Interactively prompt the user to choose a tree or handling mode. Falls back to "error" in non-interactive sessions. "first": Use the first tree "last": Use the last tree "random": Use a randomly selected tree "all": Return all trees (as multiPhylo) "split": Return all trees (as multiPhylo); callers write per-tree outputs with numeric suffixes (e.g. output_1.pdf)

Details

Newick labels longer than 500 characters are automatically truncated to 400 characters plus a ⁠_RCLADE_TRUNC⁠ suffix (with a warning), because ape's Newick parser aborts the whole R process on labels longer than ~512 characters on Linux. Truncated labels may no longer match external taxonomy files or sequence IDs; shorten labels upstream if exact matching is required.

Value

phylo object (or multiPhylo if multi_tree_mode = "all" or "split")

Rclade documentation built on Sept. 26, 2026, 5:07 p.m.