R. Page, A Taxonomic Search Engine: federating taxonomic databases using web services, BMC Bioinformatics, vol.6, issue.1, p.48, 2005.
DOI : 10.1186/1471-2105-6-48

M. Sanderson, M. Donoghue, W. Piel, and T. Eriksson, TreeBASE: a prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life, p.183, 1994.

R. Page, TBMap: a taxonomic perspective on the phylogenetic database TreeBASE, BMC Bioinformatics, vol.8, issue.1, p.158, 2007.
DOI : 10.1186/1471-2105-8-158

M. Sanderson and A. Driskell, The challenge of constructing large phylogenetic trees, Trends in Plant Science, vol.8, issue.8, pp.374-379, 2003.
DOI : 10.1016/S1360-1385(03)00165-1

L. Duret, D. Mouchiroud, and M. Gouy, HOVERGEN: a database of homologous vertebrate genes, Nucleic Acids Research, vol.22, issue.12, pp.2360-2365, 1994.
DOI : 10.1093/nar/22.12.2360

URL : https://hal.archives-ouvertes.fr/hal-00698069

J. Ruan, H. Li, Z. Chen, A. Coghlan, L. Coin et al., TreeFam: 2008 Update, Nucleic Acids Research, vol.36, issue.Database, pp.735-740, 2008.
DOI : 10.1093/nar/gkm1005

V. Ranwez, F. Delsuc, S. Ranwez, K. Belkhir, M. Tilak et al., 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

T. Hubbard, B. Aken, S. Ayling, B. Ballester, K. Beal et al., Ensembl 2009, Nucleic Acids Research, vol.37, issue.Database, pp.690-697, 2009.
DOI : 10.1093/nar/gkn828

D. Wheeler, C. Chappey, A. Lash, D. Leipe, T. Madden et al., Database resources of the National Center for Biotechnology Information, Database resources of the National Center for Biotechnology Information, pp.10-14, 2000.
DOI : 10.1093/nar/28.1.10

J. Fredslund and . Phy, FI: fast and easy online creation and manipulation of phylogeny color figures, BMC Bioinformatics, vol.7, issue.1, p.315, 2006.
DOI : 10.1186/1471-2105-7-315

G. Jordan and W. Piel, PhyloWidget: web-based visualizations for the tree of life, Bioinformatics, vol.24, issue.14, pp.1641-1642, 2008.
DOI : 10.1093/bioinformatics/btn235

R. Page, TreeView: an application to display phylogenetic trees on personal computers, Comput Appl Biosci, vol.12, pp.357-358, 1996.

F. Chevenet, C. Brun, A. Banuls, B. Jacq, and C. R. , TreeDyn: towards dynamic graphics and annotations for analyses of trees, BMC Bioinformatics, vol.7, issue.1, p.439, 2006.
DOI : 10.1186/1471-2105-7-439

URL : https://hal.archives-ouvertes.fr/hal-00321061

D. Huson, D. Richter, C. Rausch, T. Dezulian, M. Franz et al., Dendroscope: An interactive viewer for large phylogenetic trees, BMC Bioinformatics, vol.8, issue.1, p.460, 2007.
DOI : 10.1186/1471-2105-8-460

I. Letunic and P. Bork, Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation, Bioinformatics, vol.23, issue.1, pp.127-128, 2007.
DOI : 10.1093/bioinformatics/btl529

D. Chen, J. Burleigh, M. Bansal, and D. Fernandez-baca, PhyloFinder: An intelligent search engine for phylogenetic tree databases, BMC Evolutionary Biology, vol.8, issue.1, p.90, 2008.
DOI : 10.1186/1471-2148-8-90

D. Dalevi, T. Desantis, J. Fredslund, G. Andersen, V. Markowitz et al., Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool, BMC Bioinformatics, vol.8, issue.1, p.402, 2007.
DOI : 10.1186/1471-2105-8-402

M. Derthick, Interactive visualization software for exploring phylogenetic trees and clades, Bioinformatics, vol.24, issue.6, pp.868-869, 2008.
DOI : 10.1093/bioinformatics/btn038

C. Creevey and J. Mcinerney, Clann: investigating phylogenetic information through supertree analyses, Bioinformatics, vol.21, issue.3, pp.390-392, 2005.
DOI : 10.1093/bioinformatics/bti020

M. Sanderson, D. Boss, D. Chen, K. Cranston, and A. Wehe, The PhyLoTA Browser: Processing GenBank for Molecular Phylogenetics Research, iSpecies: a Species Search Engine, pp.335-346, 2008.
DOI : 10.1080/10635150802158688

C. Dunn, A. Hejnol, D. Matus, K. Pang, W. Browne et al., Broad phylogenomic sampling improves resolution of the animal tree of life, Nature, vol.22, issue.7188, pp.745-749, 2008.
DOI : 10.1038/nature06614

F. Delsuc, H. Brinkmann, D. Chourrout, and P. H. , Tunicates and not cephalochordates are the closest living relatives of vertebrates, Nature, vol.13, issue.7079, pp.965-968, 2006.
DOI : 10.1038/nature04336

URL : https://hal.archives-ouvertes.fr/halsde-00315436

B. Roure, N. Rodriguez-ezpeleta, and P. H. , SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics, BMC Evolutionary Biology, vol.7, issue.Suppl 1, p.2, 2007.
DOI : 10.1186/1471-2148-7-S1-S2

F. Delsuc, M. Scally, O. Madsen, M. Stanhope, W. De-jong et al., Molecular Phylogeny of Living Xenarthrans and the Impact of Character and Taxon Sampling on the Placental Tree Rooting, Molecular Biology and Evolution, vol.19, issue.10, pp.1656-1671, 2002.
DOI : 10.1093/oxfordjournals.molbev.a003989

URL : https://hal.archives-ouvertes.fr/halsde-00192981

R. Ricklefs, Estimating diversification rates from phylogenetic information, Trends in Ecology & Evolution, vol.22, issue.11, pp.601-610, 2007.
DOI : 10.1016/j.tree.2007.06.013