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mutalyzer-algebra
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=================
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A Boolean Algebra for Genetic Variants
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A set of Boolean relations: equivalence; containment, i.e., either a
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variant is fully contained in another or a variant fully contains another;
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overlap, i.e., two variants have (at least) one common element; and
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disjoint, i.e., no common elements that allows for a comprehensive
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classification of the relation for every pair of variants by taking all
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minimal Longest Common Subsequence (LCS) alignments into account.
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This library enables efficient handling of genomic variants based on all minimal LCS alignments.
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Publications
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------------
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The concept of binary relations between variants is introduced in:
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[Jonathan K. Vis, Mark A. Santcroos, Walter A. Kosters and Jeroen F.J. Laros.
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"A Boolean Algebra for Genetic Variants." *Bioinformatics* 39.1 (2023).](https://doi.org/10.1093/bioinformatics/btad001)
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The process of selecting a proper variant description (variant extraction) is presented in:
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[Mark A. Santcroos, Walter A. Kosters, Mihai Lefter, Jeroen F.J. Laros, Jonathan K. Vis.
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"A Graph-based Approach to Variant Extraction." *arXiv* (2025).](https://arxiv.org/abs/2503.18472)
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