Whole genome alignments include sequence alignments between two species ('pairwise alignments'), and multi-species alignments incorporating genomes of more than two species (Figure 7). Analysis of the pairwise alignments results in syntenic regions (i.e. where the sequence and gene order is conserved between two species). To infer evolutionary relationships between species, phylogenetic gene trees (or protein trees) are constructed, resulting in homologues.
Figure 7. A sampling of comparative genomics views is shown.