Homologous genes or proteins are derived from a common ancestral sequence.

Furthermore, even if an extant DNA sequence is functionless, it does not follow that it has descended from an ancestral sequence of functional DNA.

Scoring of the sequence alignment is done by comparing each of the player-aligned sequences with an algorithm-determined ancestral sequence generated at each node.

(Protein homologs have similar amino acid sequences and derive from a common ancestral sequence).

While the multiple repeats have yet to be related to any known function of the actin-severing proteins, the superfamily appears to have evolved from an ancestral sequence of 120 to 130 amino acid residues.

This allows R:S calculations to be applied to viral sequences whose ancestral sequence is unclear or unknown.

By reversing known mutations in a Y-chromosome lineage, a hypothetical ancestral sequence for the MRCA, Y-chromosomal Adam, can be inferred.

Before they used the program to reconstruct the ancestral sequence, the scientists first carried out a series of statistical tests to see how confident they could be in their program.

Of course, the ancestral sequence is usually unknown, and two lineages being compared will have been evolving in parallel since their last common ancestor.

It has been noted that the sequences translated from this locus and from that of β-actin are very similar to the predicted ones, suggesting a common ancestral sequence that suffered duplication and genetic conversion.