H. Ashkenazy, Multiple sequence alignment averaging improves phylogeny reconstruction, Syst. Biol, vol.68, pp.117-130, 2018.

V. Berry and O. Gascuel, On the interpretation of bootstrap trees: appropriate threshold of clade selection and induced gain, Mol. Biol. Evol, vol.13, pp.999-1011, 1996.

B. P. Blackburne and S. Whelan, Class of multiple sequence alignment algorithm affects genomic analysis, Mol. Biol. Evol, vol.30, pp.642-653, 2013.

D. Brawand, The evolution of gene expression levels in mammalian organs, Nature, vol.478, pp.343-348, 2011.

S. Capella-gutiérrez, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, pp.1972-1973, 2009.

J. Castresana, Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis, Mol. Biol. Evol, vol.17, pp.540-552, 2000.

J. Chang, TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction, Mol. Biol. Evol, vol.31, pp.1625-1637, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00977584

J. M. Chang, TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction, Nucleic Acids Res, vol.43, pp.3-6, 2015.
URL : https://hal.archives-ouvertes.fr/lirmm-01283940

M. Chatzou, Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty, Syst. Biol, vol.67, pp.997-1009, 2018.
URL : https://hal.archives-ouvertes.fr/lirmm-02078444

M. Chatzou, Multiple sequence alignment modeling: methods and applications, Brief. Bioinform, vol.17, pp.1009-1023, 2016.

M. O. Dayhoff, A model of evolutionary change in proteins, National Biomedical Research Foundation, pp.345-352, 1978.

F. Delsuc, Phylogenomics and the reconstruction of the tree of life, Nat. Rev. Genet, vol.6, pp.361-375, 2005.
URL : https://hal.archives-ouvertes.fr/halsde-00193293

C. Dessimoz and M. Gil, Phylogenetic assessment of alignments reveals neglected tree signal in gaps, Genome Biol, vol.11, p.37, 2010.

C. B. Do, ProbCons: probabilistic consistency-based multiple sequence alignment, Genome Res, vol.15, pp.330-340, 2005.

R. C. Edgar, MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, vol.5, pp.1-19, 2004.

J. Felsenstein, Confidence Limits on Phylogenies: an Approach Using the Bootstrap. Evolution, p.783, 1985.

F. Gascuel, How Ecology and Landscape Dynamics Shape Phylogenetic Trees, Syst. Biol, vol.64, pp.590-607, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01176270

R. L. Graham and L. R. Foulds, Unlikelihood that minimal phylogenies for a realistic biological study can be constructed in reasonable computational time, Math. Biosci, vol.60, pp.133-142, 1982.

S. Guindon, New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst. Biol, vol.59, pp.307-321, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

M. T. Holder, A justification for reporting the majority-rule consensus tree in Bayesian phylogenetics, Syst. Biol, vol.57, pp.814-821, 2008.

K. Katoh, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Res, vol.30, pp.3059-3066, 2002.

S. Kumar, MEGA X: molecular Evolutionary Genetics Analysis across Computing Platforms, Mol. Biol. Evol, vol.35, pp.1547-1549, 2018.

G. Landan and D. Graur, Heads or tails: a simple reliability check for multiple sequence alignments, Mol. Biol. Evol, vol.24, pp.1380-1383, 2007.

G. Landan and D. Graur, Local Reliability Measures From Sets of Co-optimal Multiple Sequence Alignments, Pac. Symp. Biocomput, vol.13, pp.15-24, 2008.

F. Lemoine, Renewing Felsenstein's phylogenetic bootstrap in the era of big data, Nature, vol.556, pp.452-456, 2018.
URL : https://hal.archives-ouvertes.fr/lirmm-02078445

K. Liu, Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees, Science, vol.324, pp.1561-1564, 2009.

A. Lö-ytynoja and N. Goldman, Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis, Science, vol.320, pp.1632-1635, 2008.

A. Lö-ytynoja and N. Goldman, Uniting alignments and trees, Science, vol.324, pp.1528-1529, 2009.

C. Magis, T-RMSD: a fine-grained, structure-based classification method and its application to the functional characterization of TNF receptors, J. Mol. Biol, vol.400, pp.605-617, 2010.

B. Morgenstern, DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment, Bioinformatics, vol.15, pp.211-218, 1999.

C. Notredame, T-coffee: a novel method for fast and accurate multiple sequence alignment, J. Mol. Biol, vol.302, pp.205-217, 2000.

O. Penn, An alignment confidence score capturing robustness to guide tree uncertainty, Mol. Biol. Evol, vol.27, pp.1759-1767, 2010.

O. Penn, GUIDANCE: a web server for assessing alignment confidence scores, Nucleic Acids Res, vol.38, pp.23-28, 2010.

B. D. Redelings and M. A. Suchard, Joint Bayesian estimation of alignment and phylogeny, Syst. Biol, vol.54, pp.401-418, 2005.

D. F. Robinson and L. R. Foulds, Comparison of phylogenetic trees, Math. Biosci, vol.53, pp.131-147, 1981.

A. Rokas, Genome-scale approaches to resolving incongruence in molecular phylogenies, Nature, vol.425, pp.798-804, 2003.

E. O. Romero-severson, Phylogenetically resolving epidemiologic linkage, Proc. Natl. Acad. Sci. USA, vol.113, pp.2690-2695, 2016.

K. Saurabh, Gaps: an Elusive Source of Phylogenetic Information, Syst. Biol, vol.61, pp.1075-1082, 2012.

H. A. Schmidt, TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing, Bioinformatics, vol.18, pp.502-504, 2002.

H. Shimodaira, An approximately unbiased test of phylogenetic tree selection, Syst. Biol, vol.51, pp.492-508, 2002.

T. Sing, ROCR: visualizing classifier performance in R, Bioinformatics, vol.21, pp.3940-3941, 2005.

A. Stamatakis, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, pp.2688-2690, 2006.

J. Stoye, Multiple sequence alignment with the Divide-and-Conquer method, Gene, vol.211, pp.45-56, 1998.

G. Talavera and J. Castresana, Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments, Syst. Biol, vol.56, pp.564-577, 2007.

J. Taly, Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures, Nat. Protoc, vol.6, pp.1669-1682, 2011.

G. Tan, Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference, Syst. Biol, vol.64, pp.778-791, 2015.

J. D. Thompson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res, vol.22, pp.4673-4680, 1994.

I. Ullah, Integrating sequence evolution into probabilistic orthology analysis, Syst. Biol, vol.64, pp.969-982, 2015.

I. M. Wallace, M-Coffee: combining multiple sequence alignment methods with T-Coffee, Nucleic Acids Res, vol.34, pp.1692-1699, 2006.

K. M. Wong, Alignment uncertainty and genomic analysis, Science, vol.319, pp.473-476, 2008.

A. Zharkikh and W. H. Li, Estimation of confidence in phylogeny: the complete-and-partial bootstrap technique, Mol. Phylogenet. Evol, vol.4, pp.44-63, 1995.

A. Zhukova, The Role of Phylogenetics as a Tool to Predict the Spread of Resistance, J. Infect. Dis, vol.216, pp.820-823, 2017.
URL : https://hal.archives-ouvertes.fr/lirmm-02078446