Comparative genomics analyses performed by Ensembl allow you to directly compare included species across over 50 mostly chordate genomes. Whole genome aligments, homologues arising from gene trees, protein families, and synteny are available.
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.