Sequence Alignment & Comparison

Mathematica includes state-of-the-art algorithms for sequence alignment and comparison, capable of handling strings and lists containing very large numbers of elements.

ReferenceReference

SequenceAlignment find alignments between sequences, allowing insertion and deletion

LongestCommonSubsequence find the longest contiguous subsequence in common

LongestCommonSequence find the longest sequence in common, perhaps disjoint

Similarity and Distance Measures »

SmithWatermanSimilarity ▪ NeedlemanWunschSimilarity

EditDistance ▪ DamerauLevenshteinDistance ▪ HammingDistance ▪ ...

Nearest find sequences nearest with respect to a distance measure

FindClusters find clusters of sequences with respect to a distance measure

GenomeLookup find exact matches with human and other genomes

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