A. Dereeper, V. Guignon, G. Blanc, S. Audic, S. Buffet et al., Phylogeny. fr: robust phylogenetic analysis for the non-specialist, Nucleic Acids Res, vol.36, pp.465-469, 2008.
URL : https://hal.archives-ouvertes.fr/lirmm-00324099

K. Katoh and D. M. Standley, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol, vol.30, pp.772-780, 2013.

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, Syst. Biol, vol.59, pp.307-321, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

V. Lefort, R. Desper, and O. Gascuel, FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program, Mol. Biol. Evol, vol.32, pp.2798-2800, 2015.
URL : https://hal.archives-ouvertes.fr/lirmm-01283927

F. Lemoine, J. Domelevo-entfellner, E. Wilkinson, D. Correia, M. Dàvila-felipe et al., 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

M. A. Miller, W. Pfeiffer, and T. Schwartz, Creating the CIPRES Science Gateway for inference of large phylogenetic trees, Gateway Computing Environments Workshop (GCE), pp.1-8, 2010.

A. Boc, A. B. Diallo, and V. Makarenkov, T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks, Nucleic Acids Res, vol.40, pp.573-579, 2012.

R. Sánchez, F. Serra, J. Tárraga, I. Medina, J. Carbonell et al., Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing, Nucleic Acids Res, vol.39, pp.470-474, 2011.

M. Gouy, S. Guindon, and O. Gascuel, SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building, Mol. Biol. Evol, vol.27, pp.221-224, 2009.
URL : https://hal.archives-ouvertes.fr/lirmm-00511794

S. Kumar, G. Stecher, M. Li, C. Knyaz, and K. Tamura, MEGA X: molecular evolutionary genetics analysis across computing platforms, Mol. Biol. Evol, vol.35, pp.1547-1549, 2018.

J. Goecks, A. Nekrutenko, and J. Taylor, Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome Biol, vol.11, p.86, 2010.

E. Afgan, D. Baker, B. Batut, M. Van-den-beek, D. Bouvier et al., The Galaxy platform for accessible, reproducible and collaborative biomedical analyses, vol.46, pp.537-544, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01360125

T. H. Oakley, M. A. Alexandrou, R. Ngo, M. S. Pankey, C. K. Churchill et al., Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system, BMC Bioinformatics, p.230, 2014.

E. Lord, M. Leclercq, A. Boc, A. B. Diallo, and V. Makarenkov, Armadillo 1.1: an original workflow platform for designing and conducting phylogenetic analysis and simulations, PLoS One, vol.7, p.29903, 2012.

A. Guang, F. Zapata, M. Howison, C. E. Lawrence, and C. W. Dunn, An integrated perspective on phylogenetic workflows, Trends Ecol. Evol, vol.31, pp.116-126, 2016.

F. Sievers, A. Wilm, D. Dineen, T. J. Gibson, K. Karplus et al., Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega, Mol. Syst. Biol, vol.7, p.539, 2011.

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004.

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

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 Evol. Biol, vol.10, p.210, 2010.

A. W. Dress, C. Flamm, G. Fritzsch, S. Grünewald, M. Kruspe et al., Noisy: identification of problematic columns in multiple sequence alignments, Algorith. Mol. Biol, vol.3, p.7, 2008.

S. Capella-gutiérrez, J. M. Silla-martínez, and T. Gabaldón, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, pp.1972-1973, 2009.

M. N. Price, P. S. Dehal, and A. P. Arkin, FastTree 2-approximately maximum-likelihood trees for large alignments, PLoS One, vol.5, p.9490, 2010.

P. A. Goloboff, J. S. Farris, and K. C. Nixon, TNT, a free program for phylogenetic analysis, Cladistics, vol.24, pp.774-786, 2008.

, Nucleic Acids Research, vol.47, p.265, 2019.

V. Lefort, J. Longueville, and O. Gascuel, SMS: smart model selection in PhyML, Mol. Biol. Evol, vol.34, pp.2422-2424, 2017.
URL : https://hal.archives-ouvertes.fr/lirmm-01794206

F. Ronquist, M. Teslenko, P. Van-der-mark, D. L. Ayres, A. Darling et al., MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space, Syst. Biol, vol.61, pp.539-542, 2012.

T. Junier and E. M. Zdobnov, The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell, Bioinformatics, vol.26, pp.1669-1670, 2010.

G. Tan, M. Muffato, C. Ledergerber, J. Herrero, N. Goldman et al., Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference, Syst. Biol, vol.64, pp.778-791, 2015.

G. Yachdav, S. Wilzbach, B. Rauscher, R. Sheridan, I. Sillitoe et al., MSAViewer: interactive JavaScript visualization of multiple sequence alignments, Bioinformatics, vol.32, pp.3501-3503, 2016.

S. D. Shank, S. Weaver, and S. L. Pond, ) phylotree.js--a JavaScript library for application development and interactive data visualization in phylogenetics, BMC Bioinformatics, vol.19, p.276, 2018.

I. Letunic and P. Bork, Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees, Nucleic Acids Res, vol.44, pp.242-245, 2016.

A. Dereeper, S. Audic, J. Claverie, and G. Blanc, BLAST-EXPLORER helps you building datasets for phylogenetic analysis, BMC Evol. Biol, vol.10, 2010.

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J. Mol. Biol, vol.215, pp.403-410, 1990.

F. Mareuil, O. Doppelt-azeroual, and H. Ménager, A public Galaxy platform at Pasteur used as an execution engine for web services, 1000.

C. Sloggett, N. Goonasekera, and E. Afgan, BioBlend: automating pipeline analyses within Galaxy and CloudMan, Bioinformatics, vol.29, pp.1685-1686, 2013.