PAGAN is a general-purpose method for the alignment of sequence graphs. PAGAN is based on the phylogeny-aware progressive alignment algorithm and uses graphs to describe the uncertainty in the presence of characters at certain sequence positions.
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Bioinformatics. 2012 Jul 1;28(13):1684-91. doi: 10.1093/bioinformatics/bts198. Epub 2012 Apr 23.
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.
Löytynoja A1, Vilella AJ, Goldman N.