package phylogenetics

is_stop_codon c is true if c is a stop codon.

Example :

let codon_option = Codon.of_string "TAA" in
match codon_option with
| None -> failwith "Invalid codon string"
| Some codon ->
  assert (Codon.is_stop_codon codon = true)

A stop codon is a specific codon in the genetic code that signals the termination of protein synthesis. When a stop codon is encountered during translation, the ribosome releases the newly synthesized polypeptide chain and the translation process comes to a halt. In the universal genetic code, there are three stop codons: "TAA", "TAG", and "TGA". These codons do not encode any amino acid and serve as termination signals for the protein synthesis machinery.

aa_of_codon c is -- it exists -- the amino acid encoded by c

let codon = Codon.of_string "ATG" in
let amino_acid_option = Codon.aa_of_codon codon in
match amino_acid_option with
| Some amino_acid -> assert (amino_acid = Amino_acid.Met)
| None -> failwith "No matching amino acid found"

Tests if two codons are synonymous.

Example :

let codon1_option = Codon.of_string "ATG" in
let codon2_option = Codon.of_string "ATA" in
match codon1_option, codon2_option with
| None, _ | _, None -> failwith "Invalid codon string"
| Some codon1, Some codon2 ->
  assert (Codon.synonym codon1 codon2 = false)

In this example, the codons are compared to check if they are synonymous. Two codons are synonymous if they encode the same amino acid.