A phylogenetic analysis of a family of related nucleic acid or protein sequences is a determination of how the family might have been derived during evolution. The evolutionary relationships among the sequences are represented as branches on a tree whose length and shape must be discovered. Function, structural and evolutionary information can be inferred from the alignment of biological sequences. If two sequences from different organisms are similar, there may have been a common ancestor sequence and the sequences can be defined as homologous. The alignment indicates the changes (mismatches) that could have occurred between the two homologous sequences and a common ancestor sequence during evolution (the distance x+y is known but the ancestor is not available).