Multiple sequence alignment

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Jointly align multiple sequences at once. Several heuristics are needed to achieve this in reasonable time as the problem scales exponentially with the number of sequences.

Several tools for multiple sequence alignment (MSA) exist and are supported by BioPerl including:

There also are also applications for alignment in the EMBOSS package, such as needle and water. All EMBOSS applications can be run by BioPerl in bioperl-run.

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