Phylogenetics of proteins
To study the phylogenetic releation of two proteins, we can align the amino acid sequence as well as the underlying nucleotide coding sequence. The functionality of a protein is reflected in its amino acid sequence; therefore the nucleotide sequence is usually converted into the amino acid sequence analogous to the translation. A point mutation in the DNA sequence does not necessarily lead to a change in the peptide chain because several different codons can be translated into the same amino acid. Conversely, a single nucleotide insertion might appear as a minor change on the DNA level, however, on the protein level, the nucleotide insertion can cause a shift in the whole codon pattern and therefore the sequence will be translated into a completely different amino acid sequence. Thus the amino acid sequences of the different proteins are compared with each other.