[ssml] structural alignment + multiple alignment

Kevin Karplus karplus at soe.ucsc.edu
Thu Dec 11 22:47:32 EST 2003

When I need to add more sequences to an existing multiple alignment, I
make an HMM out of the alignment then align the new sequences to the HMM.

In the a2m format that the SAM package uses, two multiple alignment
files can be concatenated if they have the same number of alignment
columns, so the initial seed alignment and the new sequences are
easily merged.

Note that this procedure will never ADD new alignment columns, so if
the new sequences have a common insertion relative to the old ones,
the inserted parts will not be aligned with respect to one another.

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