validate_tree_sequence_match: Cross-validate tree tip labels against sequence IDs

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

Cross-validate tree tip labels against sequence IDs

Description

Checks that all tree tips have corresponding sequences and vice versa.

Usage

validate_tree_sequence_match(
  tree,
  sequence_file,
  quiet = FALSE,
  mol_type = NULL,
  skip_length_check = FALSE,
  multi_tree_mode = "error"
)

Arguments

tree	phylo object or path to tree file.
sequence_file	Character. Path to sequence file (FASTA/FASTQ).
quiet	Logical. If TRUE, suppress messages.
mol_type	Character. Molecule type for sequence validation: "DNA", "RNA", "protein", or "auto" (NULL). Default: NULL.
skip_length_check	Logical. If TRUE, skip alignment length consistency check. Default: FALSE.
multi_tree_mode	Character. How to handle multiple trees in a file when tree is a path. Default: "error".

Value

List with match status and differences.

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