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
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).