(1) Department of Biology, The University of New Mexico, Albuquerque, NM, USA
Abstract:
Background
Existing sequence alignment algorithms assume that similarities between DNA or amino acid sequences are linearly ordered.
That is, stretches of similar nucleotides or amino acids are in the same order in both sequences. Recombination perturbs this
order. An algorithm that can reconstruct sequence similarity despite rearrangement would be helpful for reconstructing the
evolutionary history of recombined sequences.