. Altschul, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

. Buck, Brook for GPUs, ACM Transactions on Graphics, vol.23, issue.3, pp.777-786, 2004.
DOI : 10.1145/1015706.1015800

. Charalambous, Initial Experiences Porting a Bioinformatics Application to a Graphics Processor, Advances in Informatics, pp.415-425, 2005.
DOI : 10.1007/11573036_39

. Collange, Comparaison d'algorithmes de branchements pour le simulateur de processeur graphique barra, RenPar'19 / SympA, 2009.

. Coon, B. W. Lindholm-]-coon, and J. E. Lindholm, System and method for managing divergent threads in a SIMD architecture, 2008.

S. R. Eddy, Profile hidden Markov models, Bioinformatics, vol.14, issue.9, pp.755-763, 1998.
DOI : 10.1093/bioinformatics/14.9.755

M. Farrar, Striped Smith-Waterman speeds database searches six times over other SIMD implementations, Bioinformatics, vol.23, issue.2, pp.156-161, 2007.
DOI : 10.1093/bioinformatics/btl582
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/23/2/156

M. S. Farrar, Optimizing Smith-Waterman for the Cell Broadband Engine, 2009.

H. Fatahalian, K. Fatahalian, and M. Houston, A closer look at GPUs, Communications of the ACM, vol.51, issue.10, pp.50-57, 2008.
DOI : 10.1145/1400181.1400197

P. Gelsinger, Microprocessors for the new millennium: Challenges, opportunities, and new frontiers, 2001 IEEE International Solid-State Circuits Conference. Digest of Technical Papers. ISSCC (Cat. No.01CH37177), pp.22-25, 2001.
DOI : 10.1109/ISSCC.2001.912412

M. Giraud and J. Varré, Parallel position weight matrices algorithms, International Symposium on Parallel and Distributed Computing, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00623404

. Gschwind, Synergistic Processing in Cell's Multicore Architecture, IEEE Micro, vol.26, issue.2, pp.10-24, 2006.
DOI : 10.1109/MM.2006.41

D. Gusfield, Algorithms on Strings, Trees, and Sequences, 1997.
DOI : 10.1017/CBO9780511574931

H. Henikoff, J. Henikoff, and S. Henikoff, Amino Acid Substitution Matrices form Protein Blocks, Proc. Natl. Acad. Sci. USA, pp.10915-10919, 1992.
DOI : 10.1073/pnas.89.22.10915
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC50453/pdf

. Holland, BioJava: an open-source framework for bioinformatics, Bioinformatics, vol.24, issue.18, pp.242096-2097, 2008.
DOI : 10.1093/bioinformatics/btn397

. Kurtz, Versatile and open software for comparing large genomes, Genome Biology, vol.5, issue.R12, 2004.

. Ligowski, . Rudnicki, L. Ligowski, and W. Rudnicki, An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases, 2009 IEEE International Symposium on Parallel & Distributed Processing, 2009.
DOI : 10.1109/IPDPS.2009.5160931

. Liu, GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment, IEEE International Conference on High Performance Computing, pp.363-374, 2006.
DOI : 10.1007/11945918_37

. Liu, CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units, BMC Research Notes, vol.2, issue.1, p.73, 2009.
DOI : 10.1186/1756-0500-2-73

. Liu, Cuda-meme: Accelerating motif discovery in biological sequences using cuda-enabled graphics processing units. Pattern Recognition Letters, 2010.

. Liu, Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using cuda, IEEE International Workshop on High Performance Computational Biology, 2009.

L. , S. Lorie, R. A. Strong, J. , and H. R. , Method for conditional branch execution in SIMD vector processors, 1984.

. Manavski, . Valle, S. A. Manavski, and G. Valle, CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment, BMC Bioinformatics, vol.9, issue.Suppl 2, p.9, 2008.
DOI : 10.1186/1471-2105-9-S2-S10

. Matthews, Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure, Journal of Molecular Biology, vol.288, issue.5, pp.911-940, 1999.
DOI : 10.1006/jmbi.1999.2700

G. E. Moore, Cramming More Components Onto Integrated Circuits, Proceedings of the IEEE, vol.86, issue.1, p.38, 1965.
DOI : 10.1109/JPROC.1998.658762

G. E. Moore, Progress in digital integrated electronics, Technical Digest 1975. International Electron Devices Meeting, pp.11-13, 1975.

. Nussinov, Algorithms for Loop Matchings, SIAM Journal on Applied Mathematics, vol.35, issue.1, pp.68-82, 1978.
DOI : 10.1137/0135006

L. ]. Pearson, W. Pearson, and D. Lipman, Improved tools for biological sequence comparison., Proc. Natl. Acad. Sci, pp.3244-3248, 1988.
DOI : 10.1073/pnas.85.8.2444

. Popov, Stackless KD-Tree Traversal for High Performance GPU Ray Tracing, Computer Graphics Forum, vol.24, issue.3, pp.415-424, 2007.
DOI : 10.1111/1467-8659.00508

. Reeder, pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows, Nucleic Acids Research, vol.35, issue.Web Server, pp.35-320, 2007.
DOI : 10.1093/nar/gkm258

G. Rizk and D. Lavenier, GPU accelerated RNA folding algorithm, Using Emerging Parallel Architectures for Computational Science / International Conference on Computational Science, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00637827

. Roberts, Long time-scale simulations of in vivo diffusion using GPU hardware, 2009 IEEE International Symposium on Parallel & Distributed Processing, 2009.
DOI : 10.1109/IPDPS.2009.5160930

E. Seeberg, Six-fold speed-up of smithwaterman sequence database searches using parallel processing on common microprocessors, Bioinformatics, issue.8, pp.16699-706, 2000.

N. Saitou, N. Saitou, and M. Nei, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Molecular Biololgy and Evolution, vol.4, issue.4, pp.406-425, 1987.

M. C. Trapnell and C. , Optimizing data intensive GPGPU computations for DNA sequence alignment, Parallel Computing, vol.35, issue.8-9, p.429440, 2009.
DOI : 10.1016/j.parco.2009.05.002

. Schatz, High-throughput sequence alignment using Graphics Processing Units, BMC Bioinformatics, vol.8, issue.1, p.474, 2007.
DOI : 10.1186/1471-2105-8-474
URL : http://doi.org/10.1186/1471-2105-8-474

. Shi, Accelerating error correction in high-throughput short-read dna sequencing data with cuda, IEEE International Workshop on High Performance Computational Biology, 2009.

. Smith, . Waterman, T. F. Smith, and M. S. Waterman, Identification of common molecular subsequences, Journal of Molecular Biology, vol.147, issue.1, pp.195-197, 1981.
DOI : 10.1016/0022-2836(81)90087-5

R. Staden, Methods for calculating the probabilities of finding patterns in sequences, Bioinformatics, vol.5, issue.2, pp.89-96, 1989.
DOI : 10.1093/bioinformatics/5.2.89

. Stajich, The Bioperl Toolkit: Perl Modules for the Life Sciences, Genome Research, vol.12, issue.10, pp.1611-1618, 2002.
DOI : 10.1101/gr.361602

G. Steffen, P. Steffen, and R. Giegerich, Versatile and declarative dynamic programming using pair algebras, BMC Bioinformatics, vol.6, issue.1, 2005.

. Steffen, GPU Parallelization of Algebraic Dynamic Programming, Parallel Processing and Applied Mathematics / Parallel Biocomputing Conference (PPAM / PBC 09, 2009.
DOI : 10.1007/978-3-642-14403-5_31
URL : https://hal.archives-ouvertes.fr/inria-00438219

M. A. Suchard and A. Rambaut, Many-core algorithms for statistical phylogenetics, Bioinformatics, vol.25, issue.11, pp.251370-1376, 2009.
DOI : 10.1093/bioinformatics/btp244

. Szalkowski, SWPS3 ??? fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ??86/SSE2, BMC Research Notes, vol.1, issue.1, p.107, 2008.
DOI : 10.1186/1756-0500-1-107

V. Touzet, H. Touzet, and J. Varré, Efficient and accurate P-value computation for Position Weight Matrices, Algorithms for Molecular Biology, vol.2, issue.1, 2007.
DOI : 10.1186/1748-7188-2-15
URL : https://hal.archives-ouvertes.fr/inria-00270263

S. Trendall, C. Trendall, and A. J. Stewart, General calculations using graphics hardware, with application to interactive caustics, Proceedings of the Eurographics Workshop on Rendering Techniques, pp.287-298, 2000.
DOI : 10.1007/978-3-7091-6303-0_26
URL : https://hal.archives-ouvertes.fr/inria-00510058

. Varré, Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics, Bioinformatics Open Source Conference (BOSC), 2009.

. Walters, Evaluating the use of GPUs in liver image segmentation and HMMER database searches, 2009 IEEE International Symposium on Parallel & Distributed Processing, pp.1-12, 2009.
DOI : 10.1109/IPDPS.2009.5161073

. Wirawan, CBESW: Sequence Alignment on the Playstation 3, BMC Bioinformatics, vol.9, issue.1, 2008.
DOI : 10.1186/1471-2105-9-377

A. Wozniak, Using video-oriented instructions to speed up sequence comparison, Bioinformatics, vol.13, issue.2, pp.145-150, 1997.
DOI : 10.1093/bioinformatics/13.2.145