@article{Abouelhoda2004,
  doi={10.1016/S1570-8667(03)00065-0},
  title={Replacing suffix trees with enhanced suffix arrays},
  author={Abouelhoda, Mohamed Ibrahim and Kurtz, Stefan and Ohlebusch, Enno},
  journal={Journal of Discrete Algorithms},
  volume={2},
  number={1},
  pages={53--86},
  year={2004},
  publisher={Elsevier}
}

@article{Aho1975,
  doi={10.1145/360825.360855},
  title={Efficient string matching: an aid to bibliographic search},
  author={Aho, Alfred V and Corasick, Margaret J},
  journal={Communications of the ACM},
  volume={18},
  number={6},
  pages={333--340},
  year={1975},
  publisher={ACM}
}

@article{Altschul1990,
  doi={10.1016/S0022-2836(05)80360-2},
  title={Basic local alignment search tool},
  author={Altschul, Stephen F and Gish, Warren and Miller, Webb and Myers, Eugene W and Lipman, David J},
  journal={Journal of molecular biology},
  volume={215},
  number={3},
  pages={403--410},
  year={1990},
  publisher={Elsevier}
}

@article{Anson1997,
  doi={10.1145/267521.267524},
  title={ReAligner: a program for refining DNA sequence multi-alignments},
  author={Anson, Eric L and Myers, Eugene W},
  journal={Journal of Computational Biology},
  volume={4},
  number={3},
  pages={369--383},
  year={1997}
}

@article{BaezaYates1999,
  doi={10.1007/PL00009253},
  title={Faster approximate string matching},
  author={Baeza-Yates, Ricardo and Navarro, Gonzalo},
  journal={Algorithmica},
  volume={23},
  number={2},
  pages={127--158},
  year={1999},
  publisher={Springer}
}

@article{Brudno2003,
  doi={10.1101/gr.926603},
  title={LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA},
  author={Brudno, Michael and Do, Chuong B and Cooper, Gregory M and Kim, Michael F and Davydov, Eugene and Green, Eric D and Sidow, Arend and Batzoglou, Serafim and NISC Comparative Sequencing Program and others},
  journal={Genome research},
  volume={13},
  number={4},
  pages={721--731},
  year={2003},
  publisher={Cold Spring Harbor Lab}
}

@article{Brudno2003b,
  doi={10.1186/1471-2105-4-66},
  title={Fast and sensitive multiple alignment of large genomic sequences},
  author={Brudno, Michael and Chapman, Michael and G{\"o}ttgens, Berthold and Batzoglou, Serafim and Morgenstern, Burkhard},
  journal={BMC bioinformatics},
  volume={4},
  number={1},
  pages={66},
  year={2003},
  publisher={BioMed Central Ltd}
}

@article{Ferragina2001,
  doi={10.1016/S0020-0255(01)00098-6},
  title={An experimental study of a compressed index},
  author={Ferragina, Paolo and Manzini, Giovanni},
  journal={Information Sciences},
  volume={135},
  number={1},
  pages={13--28},
  year={2001},
  publisher={Elsevier}
}

@article{Giegerich2003,
  doi={10.1002/spe.535},
  title={Efficient implementation of lazy suffix trees},
  author={Giegerich, Robert and Kurtz, Stefan and Stoye, Jens},
  journal={Software: Practice and Experience},
  volume={33},
  number={11},
  pages={1035--1049},
  year={2003},
  publisher={Wiley Online Library}
}

@book{Gusfield1997,
  isbn={0-521-58519-8},
  title={Algorithms on strings, trees and sequences: computer science and computational biology},
  author={Gusfield, Dan},
  year={1997},
  publisher={Cambridge University Press}
}

@article{Horspool1980,
  doi={10.1002/spe.4380100608},
  title={Practical fast searching in strings},
  author={Horspool, R Nigel},
  journal={Software: Practice and Experience},
  volume={10},
  number={6},
  pages={501--506},
  year={1980},
  publisher={Wiley Online Library}
}

@article{Mortazavi2008,
  doi={10.1038/nmeth.1226},
  title={Mapping and quantifying mammalian transcriptomes by RNA-Seq},
  author={Mortazavi, Ali and Williams, Brian A and McCue, Kenneth and Schaeffer, Lorian and Wold, Barbara},
  journal={Nature methods},
  volume={5},
  number={7},
  pages={621--628},
  year={2008},
  publisher={Nature Publishing Group}
}

@article{Pearson1990,
  doi={10.1016/0076-6879(90)83007-V},
  title={Rapid and sensitive sequence comparison with FASTP and FASTA},
  author={Pearson, William R},
  journal={Methods in enzymology},
  volume={183},
  pages={63--98},
  year={1990},
  publisher={Elsevier}
}

@article{Manber1993,
  title={Suffix arrays: a new method for on-line string searches},
  author={Manber, Udi and Myers, Gene},
  journal={SIAM Journal on Computing},
  volume={22},
  number={5},
  pages={935--948},
  year={1993},
  publisher={SIAM}
}

@article{Myers1999,
  doi={10.1145/316542.316550},
  title={A fast bit-vector algorithm for approximate string matching based on dynamic programming},
  author={Myers, Gene},
  journal={Journal of the ACM (JACM)},
  volume={46},
  number={3},
  pages={395--415},
  year={1999},
  publisher={ACM}
}

@article{Rausch2008,
  doi={10.1093/bioinformatics/btn281},
  title={Segment-based multiple sequence alignment},
  author={Rausch, Tobias and Emde, Anne-Katrin and Weese, David and D{\"o}ring, Andreas and Notredame, Cedric and Reinert, Knut},
  journal={Bioinformatics},
  volume={24},
  number={16},
  pages={i187--i192},
  year={2008},
  publisher={Oxford Univ Press}
}

@article{Rausch2009,
  doi={10.1093/bioinformatics/btp131},
  title={A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads},
  author={Rausch, Tobias and Koren, Sergey and Denisov, Gennady and Weese, David and Emde, Anne-Katrin and D{\"o}ring, Andreas and Reinert, Knut},
  journal={Bioinformatics},
  volume={25},
  number={9},
  pages={1118--1124},
  year={2009},
  publisher={Oxford Univ Press}
}

@article{Thompson1994,
  doi={10.1093/nar/22.22.4673},
  title={CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice},
  author={Thompson, Julie D and Higgins, Desmond G and Gibson, Toby J},
  journal={Nucleic acids research},
  volume={22},
  number={22},
  pages={4673--4680},
  year={1994},
  publisher={Oxford Univ Press}
}

@article{Ukkonen1985,
  doi={10.1016/0196-6774(85)90023-9},
  title={Finding approximate patterns in strings},
  author={Ukkonen, Esko},
  journal={Journal of algorithms},
  volume={6},
  number={1},
  pages={132--137},
  year={1985},
  publisher={Elsevier}
}

@incollection{Weese2008,
  doi={10.1007/978-3-540-70720-2_29},
  title={Efficient string mining under constraints via the deferred frequency index},
  author={Weese, David and Schulz, Marcel H},
  booktitle={Advances in Data Mining. Medical Applications, E-Commerce, Marketing, and Theoretical Aspects},
  pages={374--388},
  year={2008},
  publisher={Springer}
}

@article{gotoh1982improved,
  title={An improved algorithm for matching biological sequences},
  author={Gotoh, Osamu},
  journal={Journal of molecular biology},
  volume={162},
  number={3},
  pages={705--708},
  year={1982},
  publisher={Elsevier}
}

@Inproceedings{Urgese2014,
  title={Dynamic Gap Selector: A Smith Waterman Sequence Alignment Algorithm with Affine Gap Model Optimisation},
  author={Urgese, Gianvito and Paciello, Giulia and Acquaviva, Andrea and Ficarra, Elisa and Graziano, Mariagrazia and Zamboni, Maurizio},
  booktitle = {In Proc. 2nd Int. Work-Conf. Bioinform. Biomed. Eng.(IWBBIO): 7-9 April 2014; Granada},
  year={2014},
  pages   = {1347-1358},
  publisher={Copicentro Granada SL},
  url={https://iwbbio.ugr.es/2014/papers/IWBBIO_2014_paper_143.pdf}
}

@article{cartwright2006logarithmic,
  title={Logarithmic gap costs decrease alignment accuracy},
  author={Cartwright, Reed A},
  journal={BMC bioinformatics},
  volume={7},
  number={1},
  pages={527},
  year={2006},
  publisher={BioMed Central Ltd}
}