-MSA — A GPU-based, fast and accurate algorithm for multiple sequence alignment

Armougom, 2006, Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee, Nucleic Acids Research, 34, W604, 10.1093/nar/gkl092

Blazewicz, 2007

Blazewicz, 2005, Selected combinatorial problems of computational biology, European Journal of Operational Research, 161, 585, 10.1016/j.ejor.2003.10.054

Blazewicz, 2009, Some remarks on evaluating the quality of the multiple sequence alignment based on the BAliBASE benchmark, International Journal of Applied Mathematics and Computer Science, 19, 675, 10.2478/v10006-009-0054-y

Blazewicz, 2011, Protein alignment algorithms with an efficient backtracking routine on multiple GPUs, BMC Bioinformatics, 12

Bradley, 2009, Fast statistical alignment, PLoS Computational Biology, 5, e1000392, 10.1371/journal.pcbi.1000392

Dayhoff, 1978, A model of evolutionary change in proteins, Atlas of protein sequence and structure, National Biomedical Research Foundation, 5, 345

Do, 2005, Probcons: probabilistic consistency-based multiple sequence alignment, Genome Research, 15, 330, 10.1101/gr.2821705

Edgar, 2004, Muscle: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, 32, 1792, 10.1093/nar/gkh340

Edgar, 2004, Muscle: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, 5, 113, 10.1186/1471-2105-5-113

Elias, 2006, Settling the intractability of multiple alignment, Journal of Computational Biology, 13, 1323, 10.1089/cmb.2006.13.1323

Ensembl databases—release 55 ftp://ftp.ensembl.org/pub/release-55, 2010.

Graham, 1969, Bounds on multiprocessing timing anomalies, SIAM Journal on Applied Mathematics, 17, 416, 10.1137/0117039

Henikoff, 1992, Amino acid substitution matrices from protein blocks, PNAS, 89, 10915, 10.1073/pnas.89.22.10915

Just, 2001, Computational complexity of multiple sequence alignment with sp-score, Journal of Computational Biology, 8, 615, 10.1089/106652701753307511

Kemena, 2009, Upcoming challenges for multiple sequence alignment methods in the high-throughput era, Bioinformatics, 25, 2455, 10.1093/bioinformatics/btp452

Kuo-Bin, 2003, ClustalW-MPI: ClustalW analysis using distributed and parallel computing, Bioinformatics, 19, 1585, 10.1093/bioinformatics/btg192

Y. Liu, D.L. Maskell, B. Schmidt, MSA-CUDA: multiple sequence alignment on graphics processing units with CUDA, in: 20th IEEE International Conference on Application-Specific Systems, Architectures and Processors, 2009, pp. 121–128.

Michener, 1957, A quantitative approach to a problem of classification, Evolution, 11, 490, 10.2307/2406046

Moretti, 2008, R-Coffee: a method for multiple alignment of non-coding RNA, Nucleic Acids Research, 36, 10, 10.1093/nar/gkn278

Needleman, 1970, A general method applicable to the search for similarities in the amino acid sequence of two proteins, Journal of Molecular Biology, 48, 443, 10.1016/0022-2836(70)90057-4

Notredame, 2000, T-Coffee: a novel method for multiple sequence alignments, Journal of Molecular Biology, 302, 205, 10.1006/jmbi.2000.4042

Pei, 2008, Multiple protein sequence alignment, Current Opinion in Structural Biology, 18, 382, 10.1016/j.sbi.2008.03.007

Pevzner, 2000

Poirot, 2004, 3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment, Nucleic Acids Research, 32, W37, 10.1093/nar/gkh382

Saitou, 1987, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Molecular Biology and Evolution, 4, 406

Sander, 1991, Database of homology-derived protein structures and the structural meaning of sequence alignment, Proteins, 9, 56, 10.1002/prot.340090107

Smith, 1981, Identification of common molecular subsequences, Journal of Molecular Biology, 147, 195, 10.1016/0022-2836(81)90087-5

Thompson, 1994, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, 22, 4673, 10.1093/nar/22.22.4673

Thompson, 2005, BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark, Proteins, 61, 127, 10.1002/prot.20527

Thompson, 2011, A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives, PLoS ONE, 6, e18093, 10.1371/journal.pone.0018093

Thompson, 1999, BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs, Bioinformatics, 15, 87, 10.1093/bioinformatics/15.1.87

Tommaso, 2010, Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon elastic-cloud, Bioinformatics, 26, 1903, 10.1093/bioinformatics/btq304

Wang, 1994, On the complexity of multiple sequence alignment, Journal of Computational Biology, 1, 337, 10.1089/cmb.1994.1.337

Waterman, 1995

J. Zola, X. Yang, S. Rospondek, S. Aluru, Parallel T-Coffee: a parallel multiple sequence aligner, in: Proceedings of ISCA PDCS-2007, 2007, pp. 248–253.