J. Beaulieu, R. Ree, J. Cavender-bares, G. Weiblen, and M. Donohue, Synthesizing phylogenetic knowledge for ecological research, Ecology, vol.93, issue.sp8, pp.934-947
DOI : 10.1080/10635150290102339

R. Page, Visualizing Phylogenetic Trees Using TreeView, Curr Protoc Bioinformatics, vol.17, pp.6-8, 2002.
DOI : 10.1002/0471250953.bi0602s01

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

M. Han and C. Zmasek, phyloXML: XML for evolutionary biology and comparative genomics, BMC Bioinformatics, vol.10, issue.1, p.356, 2009.
DOI : 10.1186/1471-2105-10-356

F. Chevenet, O. Croce, M. Hebrard, C. R. Berry, and V. , ScripTree: scripting phylogenetic graphics, Bioinformatics, vol.26, issue.8, pp.1125-1126, 2010.
DOI : 10.1093/bioinformatics/btq086

URL : https://hal.archives-ouvertes.fr/hal-00497209

I. Letunic and P. Bork, Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy, Nucleic Acids Research, vol.39, issue.suppl, pp.475-478, 2011.
DOI : 10.1093/nar/gkr201

S. Smits and C. Ouverney, jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web, PLoS ONE, vol.10, issue.8, p.12267, 2010.
DOI : 10.1371/journal.pone.0012267.s001

H. Zhang, S. Gao, M. Lercher, S. Hu, and W. Chen, EvolView, an online tool for visualizing, annotating and managing phylogenetic trees, Nucleic Acids Research, vol.40, issue.W1, pp.40569-572
DOI : 10.1093/nar/gks576

URL : http://doi.org/10.1093/nar/gks576

M. Charleston and D. Robertson, Preferential Host Switching by Primate Lentiviruses Can Account for Phylogenetic Similarity with the Primate Phylogeny, Systematic Biology, vol.51, issue.3, pp.528-535, 2002.
DOI : 10.1080/10635150290069940

T. Griebel, M. Brinkmeyer, and S. Bocker, EPoS: a modular software framework for phylogenetic analysis, Bioinformatics, vol.24, issue.20, pp.2399-2400, 2008.
DOI : 10.1093/bioinformatics/btn364

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

V. Ranwez, N. Clairon, F. Delsuc, S. Pourali, N. Auberval et al., PhyloExplorer: a web server to validate, explore and query phylogenetic trees, BMC Evolutionary Biology, vol.9, issue.1, p.108, 2009.
DOI : 10.1186/1471-2148-9-108

URL : https://hal.archives-ouvertes.fr/lirmm-00396040

R. Pethica, G. Barker, T. Kovacs, and J. Gough, TreeVector: Scalable, Interactive, Phylogenetic Trees for the Web, PLoS ONE, vol.5, issue.1, p.8934, 2010.
DOI : 10.1371/journal.pone.0008934.g001

J. Huerta-cepas, J. Dopazo, and T. Gabaldon, ETE: a python Environment for Tree Exploration, BMC Bioinformatics, vol.11, issue.1, p.24, 2010.
DOI : 10.1186/1471-2105-11-24

M. Goodman, J. Czelusniak, G. Moore, R. Herrera, and G. Matsuda, Fitting the Gene Lineage into its Species Lineage, a Parsimony Strategy Illustrated by Cladograms Constructed from Globin Sequences, Systematic Zoology, vol.28, issue.2, pp.132-163, 1979.
DOI : 10.2307/2412519

R. Page and M. Charleston, Trees within trees: phylogeny and historical associations, Trends in Ecology & Evolution, vol.13, issue.9, pp.356-359, 1998.
DOI : 10.1016/S0169-5347(98)01438-4

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

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei et al., MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.28, issue.10, pp.282731-2739, 2011.
DOI : 10.1093/molbev/msr121

T. Munzner, F. Guimbretière, S. Tasiran, L. Zhang, and Y. Zhou, TreeJuxtaposer, ACM Transactions on Graphics, vol.22, issue.3, pp.453-462, 2003.
DOI : 10.1145/882262.882291

R. Bouckaert, DensiTree: making sense of sets of phylogenetic trees, Bioinformatics, vol.26, issue.10, pp.1372-1373, 2010.
DOI : 10.1093/bioinformatics/btq110

J. Felsenstein, Bininda-Emonds ORP: Phylogenetic supertrees: combining information to reveal the tree of life, Phylogenetic Supertrees: combining information to reveal the tree of life, pp.978-979, 2004.

O. Bininda-emonds, R. Beck, and A. Purvis, Getting to the Roots of Matrix Representation, Systematic Biology, vol.54, issue.4, pp.668-672, 2005.
DOI : 10.1080/10635150590947113

J. Thorley and R. Page, RadCon: phylogenetic tree comparison and consensus, Bioinformatics, vol.16, issue.5, pp.486-487, 2000.
DOI : 10.1093/bioinformatics/16.5.486

J. Dutheil and B. Boussau, Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs, BMC Evolutionary Biology, vol.8, issue.1, p.255, 2008.
DOI : 10.1186/1471-2148-8-255

URL : https://hal.archives-ouvertes.fr/hal-00428202

H. Fernau, M. Kaufmann, and M. Poths, Comparing trees via crossing minimization, J Comput Syst Sci, vol.2010, issue.767, pp.593-608
DOI : 10.1007/11590156_37

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.92.4633

C. Scornavacca, V. Berry, V. Lefort, E. Douzery, and V. Ranwez, PhySIC_IST: cleaning source trees to infer more informative supertrees, BMC Bioinformatics, vol.9, issue.1, pp.413-429, 2008.
DOI : 10.1186/1471-2105-9-413

URL : https://hal.archives-ouvertes.fr/lirmm-00324069

B. Baum, Combining Trees as a Way of Combining Data Sets for Phylogenetic Inference, and the Desirability of Combining Gene Trees, Taxon, vol.41, issue.1, pp.3-10, 1992.
DOI : 10.2307/1222480

M. Ragan, Phylogenetic inference based on matrix representation of trees, Molecular Phylogenetics and Evolution, vol.1, issue.1, pp.53-58, 1992.
DOI : 10.1016/1055-7903(92)90035-F

. Fiorini, CompPhy: a web-based collaborative platform for comparing phylogenies, BMC Evolutionary Biology, vol.1, issue.1, p.253, 2014.
DOI : 10.1186/s12862-014-0253-5

URL : https://hal.archives-ouvertes.fr/lirmm-01140756