Codon entropy — codon_entropy • taxreturn

Codon entropy

codon_entropy(
  x,
  genetic_code = NULL,
  tryrc = TRUE,
  codon_filter = TRUE,
  resolve_draws = "majority",
  method = "ML"
)

Arguments

x: Sequences in DNAStringset or DNAbin format
genetic_code: A genetic code for the Amino acid translation. set to 'SGC4' for Invertebrate mitochondrial or see all known codes at Biostrings::GENETIC_CODE_TABLE
tryrc: Whether the reverse complemement should be evaluated if no frame without stop codons was found in the forward orientation.
codon_filter: Whether taxreturn::codon_filter should be run first to remove sequences containing stop codons or frameshifts.
resolve_draws: How draws should be resolved when multiple possible frames produce sequences with no stop codons. Options are "remove" to completely remove the sequence, or "majority" to pick the most common frame from the entire alignment.
method: the method employed to estimate entropy. see ?entropy::entropy for more details