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Read tree from file with automatic format detection

Source: R/read-input.R
read_tree_auto.Rd

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)

Value

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

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.