validate_sequence_deep: Deep validation of sequence files

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

Deep validation of sequence files

Description

Validates FASTA/FASTQ files: format detection, duplicate IDs, alphabet detection, and alignment length consistency.

Usage

validate_sequence_deep(
  filepath,
  expected_alphabet = NULL,
  check_alignment = FALSE
)

Arguments

filepath	Character. Path to sequence file.
expected_alphabet	Character or NULL. Expected alphabet: "DNA", "RNA", "protein", or NULL for auto-detect.
check_alignment	Logical. If TRUE, check all sequences have equal length.

Value

List with validation results.

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