C. Ane, B. Larget, D. Baum, S. Smith, and A. Rokas, Bayesian Estimation of Concordance among Gene Trees, Molecular Biology and Evolution, vol.24, issue.2, pp.412-426, 2007.
DOI : 10.1093/molbev/msl170

B. Blackburne and S. Whelan, Class of Multiple Sequence Alignment Algorithm Affects Genomic Analysis, Molecular Biology and Evolution, vol.30, issue.3, pp.642-653, 2013.
DOI : 10.1093/molbev/mss256

J. Burleigh, A. Driskell, and M. Sanderson, Supertree Bootstrapping Methods for Assessing Phylogenetic Variation among Genes in Genome-Scale Data Sets, Systematic Biology, vol.55, issue.3, pp.426-440, 2006.
DOI : 10.1080/10635150500541722

S. Capella-gutierrez, J. Silla-martinez, and T. Gabaldon, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, issue.15, pp.1972-1973, 2009.
DOI : 10.1093/bioinformatics/btp348

J. Castresana, Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis, Molecular Biology and Evolution, vol.17, issue.4, pp.540-552, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026334

J. Claude, K. Suhre, C. Notredame, J. Claverie, and C. Abergel, CaspR: a web server for automated molecular replacement using homology modelling, Nucleic Acids Research, vol.32, issue.Web Server, pp.606-609, 2004.
DOI : 10.1093/nar/gkh400

A. Criscuolo and S. Gribaldo, BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BMC Evolutionary Biology, vol.10, issue.1, p.210, 2010.
DOI : 10.1186/1471-2148-10-210

R. Desper and O. Gascuel, Theoretical Foundation of the Balanced Minimum Evolution Method of Phylogenetic Inference and Its Relationship to Weighted Least-Squares Tree Fitting, Molecular Biology and Evolution, vol.21, issue.3, pp.587-598, 2004.
DOI : 10.1093/molbev/msh049

URL : https://hal.archives-ouvertes.fr/lirmm-00108569

C. Do, M. Mahabhashyam, M. Brudno, and S. Batzoglou, ProbCons: Probabilistic consistency-based multiple sequence alignment, Genome Research, vol.15, issue.2, pp.330-340, 2005.
DOI : 10.1101/gr.2821705

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC546535

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

R. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340

URL : http://doi.org/10.1093/nar/gkh340

J. Felsenstein, PHYLIP-Phylogeny Inference Package(Version 3.2), Cladistics. p, pp.164-166, 1989.

P. Flicek, B. Aken, B. Ballester, K. Beal, E. Bragin et al., Ensembl's 10th year, Nucleic Acids Research, vol.38, issue.Database, pp.557-562, 2010.
DOI : 10.1093/nar/gkp972

URL : http://doi.org/10.1093/nar/gkp972

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-321, 2010.
DOI : 10.1093/sysbio/syq010

URL : https://hal.archives-ouvertes.fr/lirmm-00511784

S. Hartmann and T. Vision, Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?, BMC Evolutionary Biology, vol.8, issue.1, p.95, 2008.
DOI : 10.1186/1471-2148-8-95

X. Huang and W. Miller, A time-efficient, linear-space local similarity algorithm, Advances in Applied Mathematics, vol.12, issue.3, pp.337-357, 1991.
DOI : 10.1016/0196-8858(91)90017-D

D. Jones, W. Taylor, and J. Thornton, The rapid generation of mutation data matrices from protein sequences. Computer applications in the biosciences, CABIOS, vol.8, pp.275-282, 1992.

K. Katoh, K. Misawa, K. Kuma, and T. Miyata, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Research, vol.30, issue.14, pp.3059-3066, 2002.
DOI : 10.1093/nar/gkf436

K. Katoh and H. Toh, Recent developments in the MAFFT multiple sequence alignment program, Briefings in Bioinformatics, vol.9, issue.4, pp.286-298, 2008.
DOI : 10.1093/bib/bbn013

C. Kemena and C. Notredame, Upcoming challenges for multiple sequence alignment methods in the high-throughput era, Bioinformatics, vol.25, issue.19, pp.2455-2465, 2009.
DOI : 10.1093/bioinformatics/btp452

C. Kemena, J. Taly, J. Kleinjung, and C. Notredame, STRIKE: evaluation of protein MSAs using a single 3D structure, Bioinformatics, vol.27, issue.24, pp.3385-3391, 2011.
DOI : 10.1093/bioinformatics/btr587

J. Kim and M. J. , PSAR: measuring multiple sequence alignment reliability by probabilistic sampling, Nucleic Acids Research, vol.39, issue.15, pp.6359-6368, 2011.
DOI : 10.1093/nar/gkr334

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159474

G. Landan and D. Graur, Heads or Tails: A Simple Reliability Check for Multiple Sequence Alignments, Molecular Biology and Evolution, vol.24, issue.6, pp.1380-1383, 2007.
DOI : 10.1093/molbev/msm060

DOI : 10.1142/9789812776136_0003

M. Larkin, G. Blackshields, N. Brown, R. Chenna, P. Mcgettigan et al., Clustal W and Clustal X version 2.0, Clustal W and Clustal X version 2.0, pp.2947-2948, 2007.
DOI : 10.1093/bioinformatics/btm404

URL : https://hal.archives-ouvertes.fr/hal-00206210

T. Lassmann and E. Sonnhammer, Kalign--an accurate and fast multiple sequence alignment algorithm, BMC Bioinformatics, vol.6, issue.1, p.298, 2005.
DOI : 10.1186/1471-2105-6-298

D. Lipman, S. Altschul, and J. Kececioglu, A tool for multiple sequence alignment., Proceedings of the National Academy of Sciences, vol.86, issue.12, pp.4412-4415, 1989.
DOI : 10.1073/pnas.86.12.4412

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC287279

K. Liu, S. Raghavan, S. Nelesen, C. Linder, and T. Warnow, Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees, Science, vol.324, issue.5934, pp.1561-1564, 2009.
DOI : 10.1126/science.1171243

K. Liu, T. Warnow, M. Holder, S. Nelesen, J. Yu et al., SATe-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees, Systematic Biology, vol.61, issue.1, pp.90-106, 2012.
DOI : 10.1093/sysbio/syr095

Y. Liu, B. Schmidt, and D. Maskell, MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities, Bioinformatics, vol.26, issue.16, pp.1958-1964, 2010.
DOI : 10.1093/bioinformatics/btq338

A. Loytynoja and N. Goldman, Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis, Science, vol.320, issue.5883, pp.1632-1635, 2008.
DOI : 10.1126/science.1158395

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

C. Notredame and C. Abergel, Using multiple alignment methods to assess the quality of genomic data analysis Bioinformatics and Genomes: Current Perspectives Horizon Scientific Press, pp.30-50, 2003.

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

C. Notredame, L. Holm, and D. Higgins, COFFEE: an objective function for multiple sequence alignments, Bioinformatics, vol.14, issue.5, pp.407-422, 1998.
DOI : 10.1093/bioinformatics/14.5.407

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/14/5/407

O. Penn, E. Privman, G. Landan, D. Graur, and T. Pupko, An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty, Molecular Biology and Evolution, vol.27, issue.8, pp.1759-1767, 2010.
DOI : 10.1093/molbev/msq066

M. Phillips, F. Delsuc, and D. Penny, Genome-Scale Phylogeny and the Detection of Systematic Biases, Molecular Biology and Evolution, vol.21, issue.7, pp.1455-1458, 2004.
DOI : 10.1093/molbev/msh137

URL : https://hal.archives-ouvertes.fr/halsde-00193019

M. Price, P. Dehal, and A. Arkin, FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix, Molecular Biology and Evolution, vol.26, issue.7, pp.1641-1650, 2009.
DOI : 10.1093/molbev/msp077

M. Price, P. Dehal, and A. Arkin, FastTree 2 ??? Approximately Maximum-Likelihood Trees for Large Alignments, PLoS ONE, vol.5, issue.3, p.9490, 2010.
DOI : 10.1371/journal.pone.0009490.s003

F. Ren, H. Tanaka, and Y. Z. , An Empirical Examination of the Utility of Codon-Substitution Models in Phylogeny Reconstruction, Systematic Biology, vol.54, issue.5, pp.808-818, 2005.
DOI : 10.1080/10635150500354688

D. Robinson and L. Foulds, Comparison of phylogenetic trees, Mathematical Biosciences, vol.53, issue.1-2, pp.131-147, 1981.
DOI : 10.1016/0025-5564(81)90043-2

A. Rokas, B. Williams, N. King, and C. Sb, Genome-scale approaches to resolving incongruence in molecular phylogenies, Nature, vol.425, issue.6960, pp.798-804, 2003.
DOI : 10.1038/nature02053

U. Roshan and D. Livesay, Probalign: multiple sequence alignment using partition function posterior probabilities, Bioinformatics, vol.22, issue.22, pp.2715-2721, 2006.
DOI : 10.1093/bioinformatics/btl472

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

B. Rost, Twilight zone of protein sequence alignments, Protein Engineering Design and Selection, vol.12, issue.2, pp.85-94, 1999.
DOI : 10.1093/protein/12.2.85

C. Sander and R. Schneider, Database of homology-derived protein structures and the structural meaning of sequence alignment, Proteins: Structure, Function, and Genetics, vol.4, issue.1, pp.56-68, 1991.
DOI : 10.1002/prot.340090107

H. Shimodaira and M. Hasegawa, Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference, Molecular Biology and Evolution, vol.16, issue.8, pp.1114-1116, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026201

T. Sing, O. Sander, N. Beerenwinkel, and T. Lengauer, ROCR: visualizing classifier performance in R, Bioinformatics, vol.21, issue.20, pp.3940-3941, 2005.
DOI : 10.1093/bioinformatics/bti623

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/21/20/3940

J. Stoye, D. Evers, and M. F. , Rose: generating sequence families, Bioinformatics, vol.14, issue.2, pp.157-163, 1998.
DOI : 10.1093/bioinformatics/14.2.157

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

D. Swofford, PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version Version 4, 2003.

G. Talavera and J. Castresana, Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments, Systematic Biology, vol.56, issue.4, pp.564-577, 2007.
DOI : 10.1080/10635150701472164

D. Taylor and W. Piel, An Assessment of Accuracy, Error, and Conflict with Support Values from Genome-Scale Phylogenetic Data, Molecular Biology and Evolution, vol.21, issue.8, pp.1534-1537, 2004.
DOI : 10.1093/molbev/msh156

J. Thompson, P. Koehl, R. Ripp, and O. Poch, BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark, Proteins: Structure, Function, and Bioinformatics, vol.11, issue.Suppl 2, pp.127-136, 2005.
DOI : 10.1002/prot.20527

URL : https://hal.archives-ouvertes.fr/hal-00187785

J. Thompson, D. Higgins, and T. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994.
DOI : 10.1093/nar/22.22.4673

J. Thompson, P. Koehl, R. Ripp, and O. Poch, BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark, Proteins: Structure, Function, and Bioinformatics, vol.11, issue.Suppl 2, pp.127-136, 2005.
DOI : 10.1002/prot.20527

URL : https://hal.archives-ouvertes.fr/hal-00187785

L. Wang and T. Jiang, On the Complexity of Multiple Sequence Alignment, Journal of Computational Biology, vol.1, issue.4, pp.337-348, 1994.
DOI : 10.1089/cmb.1994.1.337

K. Wong, M. Suchard, and J. Huelsenbeck, Alignment Uncertainty and Genomic Analysis, Science, vol.319, issue.5862, pp.473-476, 2008.
DOI : 10.1126/science.1151532