E. Dermitzakis, A. Reymond, and S. Antonarakis, Conserved non-genic sequences ??? an unexpected feature of mammalian genomes, Nature Reviews Genetics, vol.430, issue.2, pp.151-157, 2005.
DOI : 10.1038/nature02797

D. Przybylski and B. Rost, Alignments grow, secondary structure prediction improves, Proteins: Structure, Function, and Genetics, vol.12, issue.2, pp.197-205, 2002.
DOI : 10.1093/nar/12.24.9567

A. Löytynoja and N. Goldman, Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis, Science, vol.319, issue.5862, pp.1632-1635, 2008.
DOI : 10.1126/science.1151532

R. Meredith, J. Gatesy, W. Murphy, O. Ryder, and M. Springer, Molecular Decay of the Tooth Gene Enamelin (ENAM) Mirrors the Loss of Enamel in the Fossil Record of Placental Mammals, PLoS Genetics, vol.66, issue.9, p.1000634, 2009.
DOI : 10.1371/journal.pgen.1000634.s012

K. Wong, M. Suchard, and J. Huelsenbeck, Alignment Uncertainty and Genomic Analysis, Science, vol.43, issue.25, pp.473-476, 2008.
DOI : 10.1073/pnas.2036252100

M. Margulies, M. Egholm, W. Altman, S. Attiya, and J. Bader, Genome sequencing in microfabricated high-density picolitre reactors, Nature, vol.2, issue.7057, pp.376-380, 2005.
DOI : 10.1089/cmb.1995.2.275

M. Kircher, U. Stenzel, and J. Kelso, Improved base calling for the Illumina Genome Analyzer using machine learning strategies, Genome Biology, vol.10, issue.8, p.83, 2009.
DOI : 10.1186/gb-2009-10-8-r83

M. Gilbert, J. Binladen, W. Miller, C. Wiuf, and E. Willerslev, Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis, Nucleic Acids Research, vol.35, issue.1, pp.1-10, 2007.
DOI : 10.1093/nar/gkl483

D. Zheng, A. Frankish, R. Baertsch, P. Kapranov, and A. Reymond, Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution, Genome Research, vol.17, issue.6, pp.839-851, 2007.
DOI : 10.1101/gr.5586307

P. Farabaugh, Programmed Translational Frameshifting, Annual Review of Genetics, vol.30, issue.1, pp.507-528, 1996.
DOI : 10.1146/annurev.genet.30.1.507
URL : http://europepmc.org/articles/pmc239420?pdf=render

J. Raes and Y. Van-de-peer, Functional divergence of proteins through frameshift mutations, Trends in Genetics, vol.21, issue.8, pp.428-459, 2005.
DOI : 10.1016/j.tig.2005.05.013

D. Higgins, A. Bleasby, and R. Fuchs, CLUSTAL V: improved software for multiple sequence alignment, Bioinformatics, vol.8, issue.2, pp.189-191, 1992.
DOI : 10.1093/bioinformatics/8.2.189

C. Notredame, D. Higgins, and J. Heringa, T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton, Journal of Molecular Biology, vol.302, issue.1, pp.205-217, 2000.
DOI : 10.1006/jmbi.2000.4042

B. Morgenstern, O. Rinner, S. Abdeddaim, D. Haase, and K. Mayer, Exon discovery by genomic sequence alignment, Bioinformatics, vol.18, issue.6, pp.777-787, 2002.
DOI : 10.1093/bioinformatics/18.6.777
URL : https://academic.oup.com/bioinformatics/article-pdf/18/6/777/588853/180777.pdf

R. Edgar, MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, vol.5, issue.1, p.113, 2004.
DOI : 10.1186/1471-2105-5-113

K. Katoh, K. Kuma, H. Toh, and T. Miyata, MAFFT version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Research, vol.33, issue.2, pp.511-518, 2005.
DOI : 10.1093/nar/gki198

R. Bradley, A. Roberts, M. Smoot, S. Juvekar, and J. Do, Fast Statistical Alignment, PLoS Computational Biology, vol.72, issue.5, p.1000392, 2009.
DOI : 10.1371/journal.pcbi.1000392.s001
URL : http://doi.org/10.1371/journal.pcbi.1000392

R. Wernersson and A. Pedersen, RevTrans: multiple alignment of coding DNA from aligned amino acid sequences, Nucleic Acids Research, vol.31, issue.13, pp.3537-3539, 2003.
DOI : 10.1093/nar/gkg609

O. Bininda-emonds, transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences, BMC Bioinformatics, vol.6, issue.1, p.156, 2005.
DOI : 10.1186/1471-2105-6-156

M. Suyama, D. Torrents, and P. Bork, PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments, Nucleic Acids Research, vol.34, issue.Web Server, pp.609-612, 2006.
DOI : 10.1093/nar/gkl315

F. Abascal, R. Zardoya, and M. Telford, TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations, Nucleic Acids Research, vol.24, issue.suppl_2, pp.7-13, 2010.
DOI : 10.1016/S1055-7903(02)00202-6

J. Thompson, B. Linard, O. Lecompte, and O. Poch, A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives, PLoS ONE, vol.15, issue.31, p.18093, 2011.
DOI : 10.1371/journal.pone.0018093.t001
URL : https://hal.archives-ouvertes.fr/hal-01636867

J. Hein, An Algorithm Combining DNA and Protein Alignment, Journal of Theoretical Biology, vol.167, issue.2, pp.169-174, 1994.
DOI : 10.1006/jtbi.1994.1062

L. Arvestad, Aligning coding DNA in the presence of frame-shift errors, Proceedings of the 9th Annual Symposium on Combinatorial Pattern Matching, pp.180-190, 1997.
DOI : 10.1007/3-540-63220-4_59

C. Pedersen, R. Lyngsø, and J. Hein, Comparison of coding DNA, CPM 98: combinatorial pattern matching, Lecture Notes in Computer Science, pp.153-173, 1998.

R. Stocsits, I. Hofacker, C. Fried, and P. Stadler, Multiple sequence alignments of partially coding nucleic acid sequences, BMC Bioinformatics, vol.6, issue.1, p.160, 2005.
DOI : 10.1186/1471-2105-6-160

X. Guan and E. Uberbacher, Alignments of DNA and protein sequences containing frameshift errors, Bioinformatics, vol.12, issue.1, pp.31-40, 1996.
DOI : 10.1093/bioinformatics/12.1.31

T. Smith and M. 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

S. Steiger, A. Fidler, M. Valcu, and B. Kempenaers, Avian olfactory receptor gene repertoires: evidence for a well-developed sense of smell in birds?, Proceedings of the Royal Society B: Biological Sciences, vol.11, issue.10, pp.2309-2326, 2008.
DOI : 10.1093/hmg/11.10.1153

H. Zhao, D. Xu, S. Zhang, and J. Zhang, Widespread Losses of Vomeronasal Signal Transduction in Bats, Molecular Biology and Evolution, vol.37, issue.1, pp.7-12, 2011.
DOI : 10.1093/molbev/msq152

T. Demere, M. Mcgowen, A. Berta, and J. Gatesy, Morphological and Molecular Evidence for a Stepwise Evolutionary Transition from Teeth to Baleen in Mysticete Whales, Systematic Biology, vol.18, issue.1, pp.15-37, 2008.
DOI : 10.1016/S0169-5347(03)00033-8

Y. Van-de-peer, J. Taylor, I. Braasch, and A. Meyer, The Ghost of Selection Past: Rates of Evolution and Functional Divergence of Anciently Duplicated Genes, Journal of Molecular Evolution, vol.53, issue.4-5, pp.436-446, 2001.
DOI : 10.1007/s002390010233

L. Salmela and J. Schroder, Correcting errors in short reads by multiple alignments, Bioinformatics, vol.18, issue.5, 2011.
DOI : 10.1101/gr.074492.107

H. Philippe and M. Telford, Large-scale sequencing and the new animal phylogeny, Trends in Ecology & Evolution, vol.21, issue.11, pp.614-620, 2006.
DOI : 10.1016/j.tree.2006.08.004

D. Huchon, O. Madsen, M. Sibbald, K. Ament, and M. Stanhope, Rodent Phylogeny and a Timescale for the Evolution of Glires: Evidence from an Extensive Taxon Sampling Using Three Nuclear Genes, Molecular Biology and Evolution, vol.19, issue.7, pp.1053-1065, 2002.
DOI : 10.1080/106351599260481

V. Ranwez, F. Delsuc, S. Ranwez, K. Belkhir, and M. Tilak, OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics, BMC Evolutionary Biology, vol.7, issue.1, p.241, 2007.
DOI : 10.1186/1471-2148-7-241
URL : https://hal.archives-ouvertes.fr/halsde-00315511

X. Huang and A. Madan, CAP3: A DNA Sequence Assembly Program, Genome Research, vol.9, issue.9, pp.868-877, 1999.
DOI : 10.1101/gr.9.9.868

B. Chevreux, T. Pfisterer, B. Drescher, A. Driesel, and W. Müller, Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs, Genome Research, vol.14, issue.6, pp.1147-1159, 2004.
DOI : 10.1101/gr.1917404

F. Delsuc, G. Tsagkogeorga, N. Lartillot, and P. H. , Additional molecular support for the new chordate phylogeny, genesis, vol.19, issue.7, pp.592-604, 2008.
DOI : 10.1093/oxfordjournals.molbev.a004134
URL : https://hal.archives-ouvertes.fr/halsde-00338411

T. Hubbard, B. Aken, S. Ayling, B. Ballester, and K. Beal, Ensembl 2009, Nucleic Acids Research, vol.447, issue.7145, pp.690-697, 2009.
DOI : 10.1038/nature05911
URL : https://hal.archives-ouvertes.fr/hal-01615160

M. Dayhoff, R. Schwartz, and B. Orcutt, A model of evolutionary change in proteins, Atlas of Protein Sequence and Structure, pp.345-352, 1978.

S. Henikoff and J. Henikoff, Amino acid substitution matrices from protein blocks., Proceedings of the National Academy of Sciences, vol.89, issue.22, pp.10915-10919, 1992.
DOI : 10.1073/pnas.89.22.10915

S. Altschul, Gap costs for multiple sequence alignment, Journal of Theoretical Biology, vol.138, issue.3, pp.297-309, 1989.
DOI : 10.1016/S0022-5193(89)80196-1

J. Kececioglu and D. Starrett, Aligning alignments exactly, Proceedings of the eighth annual international conference on Computational molecular biology , RECOMB '04, pp.85-96, 2004.
DOI : 10.1145/974614.974626
URL : http://www.cs.arizona.edu/~kece/Research/papers/KS04.pdf

S. Needleman and C. Wunsch, A general method applicable to the search for similarities in the amino acid sequence of two proteins, Journal of Molecular Biology, vol.48, issue.3, pp.443-453, 1970.
DOI : 10.1016/0022-2836(70)90057-4

D. Sankoff, Matching Sequences under Deletion/Insertion Constraints, Proceedings of the National Academy of Sciences, vol.69, issue.1, pp.4-6, 1972.
DOI : 10.1073/pnas.69.1.4
URL : http://www.pnas.org/content/69/1/4.full.pdf

S. Altschul and B. Erickson, Optimal sequence alignment using affine gap costs, Bulletin of Mathematical Biology, vol.82, issue.5-6, pp.603-616, 1986.
DOI : 10.1007/BF02462326

J. Kececioglu and W. Zhang, Aligning alignments, CPM '98: Proceedings of the 9th Annual Symposium on Combinatorial Pattern Matching, pp.189-208, 1998.
DOI : 10.1007/BFb0030790

T. Wheeler and J. Kececioglu, Multiple alignment by aligning alignments, Bioinformatics, vol.15, issue.13, pp.559-568, 2007.
DOI : 10.1093/bioinformatics/15.10.862
URL : https://academic.oup.com/bioinformatics/article-pdf/23/13/i559/651773/btm226.pdf

R. Edgar, Local homology recognition and distance measures in linear time using compressed amino acid alphabets, Nucleic Acids Research, vol.32, issue.1, pp.380-385, 2004.
DOI : 10.1093/nar/gkh180

P. Sneath and R. Sokal, Numerical taxonomy: the principles and practice of numerical classification, 1973.

N. Galtier, M. Gouy, and C. Gautier, SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny, Bioinformatics, vol.12, issue.6, pp.543-548, 1996.
DOI : 10.1093/bioinformatics/12.6.543
URL : https://hal.archives-ouvertes.fr/hal-00435028

M. Gouy, S. Guindon, and O. Gascuel, SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol.24, issue.8, pp.221-224, 2010.
DOI : 10.1093/molbev/msm092
URL : https://hal.archives-ouvertes.fr/lirmm-00705187