DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.

Basic local alignment search tool

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617 · see citing works

A general method applicable to the search for similarities in the amino acid sequence of two proteins

Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288 · see citing works

Improved tools for biological sequence comparison.

Pearson, W. R., & Lipman, D. J. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.8.2444 · Cited by 11,227 · see citing works

Amino acid substitution matrices from protein blocks.

Henikoff, S., & Henikoff, J. G. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.22.10915 · Cited by 6,218 · see citing works

Multiple sequence alignment with hierarchical clustering.

Corpet, F. (1988) · Nucleic Acids Research · doi:10.1093/nar/16.22.10881 · Cited by 5,575 · see citing works

Detecting Subtle Sequence Signals: a Gibbs Sampling Strategy for Multiple Alignment

Lawrence, C. E., Altschul, S. F., Boguski, M. S., Liu, J. S., Neuwald, A. F., & Wootton, J. C. (1993) · Science · doi:10.1126/science.8211139 · Cited by 1,810 · see citing works

A workbench for multiple alignment construction and analysis

Schuler, G. D., Altschul, S. F., & Lipman, D. J. (1991) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340090304 · Cited by 985 · see citing works

Comparison of biosequences

Smith, T. F., & Waterman, M. S. (1981) · Advances in Applied Mathematics · doi:10.1016/0196-8858(81)90046-4 · Cited by 677 · see citing works

SAGA: sequence alignment by genetic algorithm

Notredame, C. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.8.1515 · Cited by 512 · see citing works

DIALIGN: finding local similarities by multiple sequence alignment.

Morgenstern, B., Frech, K., Dress, A., et al. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.3.290 · Cited by 359 · see citing works

Inching toward reality: An improved likelihood model of sequence evolution

Thorne, J. L., Kishino, H., & Felsenstein, J. (1992) · Journal of Molecular Evolution · doi:10.1007/bf00163848 · Cited by 329 · see citing works

Multiple DNA and protein sequence alignment based on segment-to-segment comparison.

Morgenstern, B., Dress, A., & Werner, T. A. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.22.12098 · Cited by 300 · see citing works

Automatic generation of primary sequence patterns from sets of related protein sequences.

Smith, R. F., & Smith, T. F. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.1.118 · Cited by 289 · see citing works

On global sequence alignment

Huang, X. (1994) · Computer applications in the biosciences · doi:10.1093/bioinformatics/10.3.227 · Cited by 230 · see citing works

Comparative analysis of multiple protein-sequence alignment methods.

McClure, M. A., Vasi, T. K., & Fitch, W. M. (1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040138 · Cited by 163 · see citing works

Maximum likelihood alignment of DNA sequences

Bishop, M. J., & Thompson, E. A. (1986) · Journal of Molecular Biology · doi:10.1016/0022-2836(86)90289-5 · Cited by 148 · see citing works

Evolutionary conservation of RecA genes in relation to protein structure and function

Karlin, S., & Brocchieri, L. (1996) · Journal of Bacteriology · doi:10.1128/jb.178.7.1881-1894.1996 · Cited by 138 · see citing works

Bayesian adaptive sequence alignment algorithms.

Zhu, J. Z., Liu, J. S., & Lawrence, C. E. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.1.25 · Cited by 124 · see citing works

Multiple sequence alignment by consensus

Waterman, M. S. (1986) · Nucleic Acids Research · doi:10.1093/nar/14.22.9095 · Cited by 118 · see citing works

Detecting Patterns in Protein Sequences

Neuwald, A. F., & Green, P. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1407 · Cited by 104 · see citing works

Multiple sequence alignment with the divide-and-conquer method

Stoye, J. (1998) · Gene · doi:10.1016/s0378-1119(98)00097-3 · Cited by 95 · see citing works

A symmetric-iterated multiple alignment of protein sequences

Brocchieri, L., & Karlin, S. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1527 · Cited by 68 · see citing works

A branch-and-cut algorithm for multiple sequence alignment

Reinert, K., Lenhof, H., Mutzel, P., et al. (1997) · Annual International Conference on Research in Computational Molecular Biology (RECOMB) · doi:10.1145/267521.267845 · Cited by 67 · see citing works

A nonlinear measure of subalignment similarity and its significance levels

Altschul, S. F., & Erickson, B. W. (1986) · Bulletin of Mathematical Biology · doi:10.1007/bf02462327 · Cited by 56 · see citing works

Match-Box_server: a multiple sequence alignment tool placing emphasis on reliability

Depiereux, E., Baudoux, G., Briffeuil, P., et al. (1997) · Computer applications in the biosciences · doi:10.1093/bioinformatics/13.3.249 · Cited by 49 · see citing works

MATCH-BOX: a fundamentally new algorithm for the simultaneous alignment of several protein sequences

Depiereux, E., & Feytmans, E. (1992) · Computer applications in the biosciences · doi:10.1093/bioinformatics/8.5.501 · Cited by 46 · see citing works

An exact solution for the segment-to-segment multiple sequence alignment problem.

Lenhof, H., Morgenstern, B., & Reinert, K. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.3.203 · Cited by 43 · see citing works

Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance reliability of predictions.

Briffeuil, P., Baudoux, G., Lambert, C., Bolle, X. D., Vinals, C., Feytmans, E., & Depiereux, E. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.4.357 · Cited by 34 · see citing works

Chaining Multiple-Alignment Blocks

Zhang, Z., Raghavachari, B., Hardison, R. C., et al. (1994) · Journal of Computational Biology · doi:10.1089/cmb.1994.1.217 · Cited by 32 · see citing works

A general method for fast multiple sequence alignment

Tönges, U., Perrey, S. W., Stoye, J., et al. (1996) · Gene · doi:10.1016/0378-1119(96)00123-0 · Cited by 30 · see citing works

Estimation and Reliability of Molecular Sequence Alignments

Thorne, J. L., & Churchill, G. A. (1995) · Biometrics · doi:10.2307/2533318 · Cited by 27 · see citing works

Segment-based scores for pairwise and multiple sequence alignments.

Morgenstern, B., Atchley, W. R., Hahn, K. M., et al. (1998) · PubMed · Cited by 15 · see citing works

Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching

Amir, A., & Landau, G. M. (2001) · Cited by 5 · see citing works

A nonlinear measure of subalignment similarity and its significance levels

Altschul, S. F., & ERICKSON, B. (1986) · Bulletin of Mathematical Biology · doi:10.1016/s0092-8240(86)90011-x · Cited by 4 · see citing works

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

Katoh, K. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf436 · Cited by 17,027 · see citing works

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

Initiative, T. A. G. (2000) · Nature · doi:10.1038/35048692 · Cited by 9,301 · see citing works

Alignment Uncertainty and Genomic Analysis

Wong, K. M., Suchard, M. A., & Huelsenbeck, J. P. (2008) · Science · doi:10.1126/science.1151532 · Cited by 411 · see citing works

Evolutionary dynamics of transposable elements in the short-tailed opossum <i>Monodelphis domestica</i>

Gentles, A. J., Wakefield, M. J., Kohany, O., Gu, W., Batzer, M. A., Pollock, D. D., & Jurka, J. (2007) · Genome Research · doi:10.1101/gr.6070707 · Cited by 156 · see citing works

Electrochemical DNA synthesis and sequencing on a single electrode with scalability for integrated data storage

Xu, C., Ma, B., Gao, Z., Dong, X., Zhao, C., & Liu, H. (2021) · Science Advances · doi:10.1126/sciadv.abk0100 · Cited by 79 · see citing works

Functional Interaction between Pleiotropic Transactivator pUL69 of Human Cytomegalovirus and the Human Homolog of Yeast Chromatin Regulatory Protein SPT6

Winkler, M., aus dem Siepen, T., & Stamminger, T. (2000) · Journal of Virology · doi:10.1128/jvi.74.17.8053-8064.2000 · Cited by 59 · see citing works

Whole-Genome Alignment: Methods, Challenges, and Future Directions

Saada, B., Zhang, T., Siga, E., Zhang, J., & Magalhães Muniz, M. M. (2024) · Applied Sciences · doi:10.3390/app14114837 · Cited by 15 · see citing works

Alignment of protein sequences by their profiles

Martı́-Renom, M. A., Madhusudhan, M. S., & Šali, A. (2004) · Protein Science · doi:10.1110/ps.03379804 · Cited by 190 · see citing works

Homology-extended sequence alignment

Simossis, V. A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki233 · Cited by 116 · see citing works

Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems

Grasso, C. S., & Lee, C. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth126 · Cited by 121 · see citing works

Multiple Sequence Alignment

Zimmermann, K.-H. (2003) · Kluwer international series in engineering and computer science · doi:10.1007/978-1-4419-9210-9_4 · Cited by 1 · see citing works

INTERALIGN: interactive alignment editor for distantly related protein sequences

Pible, O., Imbert, G., & Pellequer, J. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti474 · Cited by 10 · see citing works