Whole genome alignment
Two types of pairwise genome alignment are available in Ensembl Genomes, based on LastZ  (or its predecessor BlastZ ) and translated BLAT (tBLAT) . LastZ is typically used for closely related species, and tBLAT for more distant species. The method of alignment affects the coverage of the genomes, with tBLAT expected to mostly find homologies in coding regions.
The raw results from LastZ or tBLAT are alignment blocks, which are 'chained' according to their location in both genomes, then 'netted' to choose the best sub-chain in each region for the reference species . The resultant LastZ-net and tBLAT-net alignments are displayed in Ensembl Genomes for selected fungal, metazoan, protist and plant species.
For a list of whole genome alignments available in each Ensembl Genomes division, please follow the links below: