AGE (Alignment with Gap Excision) is a tools that implements an algorithm for optimal alignment of sequences with SVs.
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Bioinformatics. 2011 Mar 1;27(5):595-603. Epub 2011 Jan 13.
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.
Abyzov A, Gerstein M.