Genomic Algorithms

This is a collection of algorithms used in genomics, implemented with python and c++.

Distance

Edit distance
Hamming distance
Levenshtein distance
Shortest detour

Alignment

Needleman Wunsch alignment
Smith Waterman alignment
Semi global alignment

Indexes

Kmer
Suffix Trie
Suffix Tree
Suffix Array
Burrows-Wheeler Transform with FM index