The MAPGAPS program uses a set of multiply-aligned profiles both as a query to detect and classify related sequences and as a template to multiply-align the sequences.
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Bioinformatics. 2009 Aug 1;25(15):1869-75. doi: 10.1093/bioinformatics/btp342. Epub 2009 Jun 8.
Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.