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. Author manuscript; available in PMC: 2019 Apr 5.
Published in final edited form as: Annu Rev Anim Biosci. 2018 Oct 31;7:41–64. doi: 10.1146/annurev-animal-020518-115005

Table 1.

Pairwise genome alignment tools

Program Year (Reference) Description
MUMmer 1999 (4, 117) Fast aligner relying on maximal unique matches from a query sequence to a reference sequence; recent versions remove the colinearity restriction of the first version and improve the speed
Chains and nets 2003 (29) Combines fragmented local alignments into larger, high-scoring chains, which are arranged into hierarchical nets representing rearrangements
Shuffle-LAGAN 2003 (27) A glocal (global + local) aligner that is less restrictive than global alignment but still enforces monotonicity of the blocks relative to one sequence