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You should never use a pairwise alignment format to hold a multiple sequence alignment as the file would be unparsable by EMBOSS and other systems.
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These are the formats to choose when the sequences are to be used by another EMBOSS application.
In such cases, the sequences given will still be in their aligned condition (i.e.
The alignment length (131) and percentage (19.1%) of positions in the alignment where there are gaps is given. For an explanation of the score schemes refer to the relevant application documentation.
Alignment inputs are referred to on the EMBOSS command line by their USA (Section 6.6, “The Uniform Sequence Address (USA)”).