The Underlying Approach (UA) builds a scoring function based on this set of patterns, called underlying. This set is by construction linear in the size of input, without overlaps, and can be efficiently constructed. Results show the validity of our method in the reconstruction of phylogenetic trees, where the Underlying Approach outperforms the current state of the art methods. Moreover, the accuracy of UA is achieved with a very small number of subwords, which in some cases carry meaningful biological information.
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Algorithms Mol Biol. 2012 Dec 6;7(1):34. doi: 10.1186/1748-7188-7-34.
Alignment-free phylogeny of whole genomes using underlying subwords.
Comin M, Verzotto D.