CoreAligner is a software for identifying the core structure of related genomes, which is defined as a set of sufficiently long segments in which gene orders are conserved among multiple genomes so that they are likely to have been inherited mainly through vertical transfer. Using a dynamic programming based algorithm, CoreAligner finds the order of pre-identified orthologous groups (OGs) that retains to the greatest possible extent the conserved gene orders.
Ikuo Uchiyama (email@example.com)
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I. Uchiyama (2008)
Multiple genome alignment for identifying the core structure among moderately related microbial genomes
BMC Genomics, 9:515.