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Development of specialised algorithms for genomic sequence alignment is nevertheless considered to be a high priority (Miller 2001; Chain et al. 2003) . ... In this sense, horizontal gene transfer can be thought of as 'nonhomologous recombination', since it involves a genomic region that is new to a genome, whereas 'homologous recombination' involves a new ... This illustrates the advantages of aligning protein-coding sequences as amino acids rather than as nucleotides. ...doi:10.1071/sb06020 fatcat:jphfjfnv3bf53fue2aadwq3xau