By using encoded protein sequences, the issues brought on by nucleotide compositional biases in DNA sequences are avoided.
The use of encoded protein sequences is thought to get around the issues brought on by nucleotide compositional biases in the DNA sequences, making phylogenetic analyses based on protein sequences compared to those derived from the comparable .
The 'signal-to-noise ratio' in protein sequence alignments is much better than in DNA sequence alignments simply because proteins are constructed from 20 amino acids while DNA only contains four different bases.
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