Sequence Alignment & Comparison

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

(RefLink[SequenceAlignment, paclet:ref/SequenceAlignment]) — find alignments between strings, allowing insertion and deletion

(RefLink[LongestCommonSubsequence, paclet:ref/LongestCommonSubsequence]) — find the longest contiguous subsequence in common

(RefLink[LongestCommonSequence, paclet:ref/LongestCommonSequence]) — find the longest sequence in common, perhaps disjoint

(RefLink[Subsequences, paclet:ref/Subsequences]) — all subsequences of a list

(RefLink[LongestOrderedSequence, paclet:ref/LongestOrderedSequence]) — find the longest ordered sequence in a list, perhaps disjoint

(OrangeLink[Similarity and Distance Measures », paclet:guide/DistanceAndSimilarityMeasures])

(RefLink[Nearest, paclet:ref/Nearest]) — find sequences nearest with respect to a distance measure

(RefLink[FindClusters, paclet:ref/FindClusters]) — find clusters of sequences with respect to a distance measure

(RefLink[DistanceMatrix, paclet:ref/DistanceMatrix]) — construct the matrix of pairwise distances

(RefLink[GenomeLookup, paclet:ref/GenomeLookup]) — find exact matches with human and other genomes