The tree is determined from the scores of pairwise alignments of the sequences. Contrast with homology. COGs - Clusters of orthologous groups. See the COGs web site for more details. All the taxa descended from a major cladogenesis event, recognized by possessing the clade's synapomorphy.
Distances are small for similar sequences.
The Protdist program we use computes a distance measure for protein sequences, using maximum likelihood estimates based on a particular matrix that indicates the significance of certain amino acid changes. When one organism takes up permanent residence within another, such that the two become a single functional organism. Mitochondria and plastids are believed to have resulted from endosymbiosis. A diagram which depicts the hypothetical phylogeny of the taxa under consideration. The points at which lineages split represent ancestor taxa to the descendant taxa appearing at the terminal points of the cladogram.