Identifying genomic homology within and between genomes is essential when studying genome evolution. In the past years, different computational techniques have been developed to detect homology even when the actual similarity between homologous segments is low. Depending on the strategy used, these methods search for pairs of chromosomal segments between which either both gene content and order are conserved or gene content only. However, due to fact that, after their divergence, homologous segments can lose a different set of genes, these methods still often fail to detect genomic homology. Recently, more advanced approaches have been developed that can combine gene order and content information of multiple genomic segments.
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