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=== Alignment === ''Generation of Recursive Analyses Linked by Dependency (GERALD)'' is the module used for sequence alignment, data visualization, filtering, and alignment. The following two alignment programs work within the GERALD module: * ''Efficient Large-Scale Alignment of Nucleotide Databases (ELAND)'' is very fast and aligns for up to two errors from a reference for the first 32 bases. This algorithm is used for any reference larger than 100 kb. * ''PhageAlign'' does an exhaustive alignment (all possible alignments up to arbitrary edit distances), but is slow.
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