V. Daubin, M. Gouy, and G. Perrì-ere, A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History, Genome Research, vol.12, issue.7, pp.1080-1090, 2002.
DOI : 10.1101/gr.187002

URL : https://hal.archives-ouvertes.fr/hal-00427259

J. Jansson, J. H. Ng, K. Sadakane, and W. K. Sung, Rooted Maximum Agreement Supertrees, Algorithmica, vol.43, issue.4, pp.293-307, 2005.
DOI : 10.1007/s00453-004-1147-5

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.103.2579

V. Berry and F. Nicolas, Maximum agreement and compatible supertrees, Journal of Discrete Algorithms, vol.5, issue.3, pp.564-591, 2007.
DOI : 10.1016/j.jda.2006.08.005

URL : https://hal.archives-ouvertes.fr/lirmm-00108782

M. Y. Kao, Encyclopedia of Algorithms, 2007.

F. J. Lapointe and L. J. Rissler, Congruence, Consensus, and the Comparative Phylogeography of Codistributed Species in California, The American Naturalist, vol.166, issue.2, pp.290-299, 2005.
DOI : 10.1086/431283

D. M. De-vienne, T. Giraud, and O. C. Martin, A congruence index for testing topological similarity between trees, Bioinformatics, vol.23, issue.23, pp.3119-3124, 2007.
DOI : 10.1093/bioinformatics/btm500

E. Jousselin, S. Van-noort, V. Berry, J. Y. Rasplus, N. Ronsted et al., One fig to binf them all: host conservatism in a fig wasp community unraveled by cospeciation analyses among pollinating and nonpollinating fig wasps, Evolution, 2008.

F. Ge, L. S. Wang, and J. Kim, The cobweb of life revealed by genomescale estimates of horizontal gene transfer, PLOS Biology, vol.3, issue.10, pp.1709-1718, 2005.

L. Nakhleh, D. Ruths, and L. S. Wang, RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer, Computating and Combinatorics, 11th Ann. Int. Conf. (COCOON)
DOI : 10.1007/11533719_11

J. Flum and M. Grohe, Parameterized Complexity Theory, 2006.

R. Agarwala and D. Fernandez-baca, A Polynomial-Time Algorithm For the Perfect Phylogeny Problem When the Number of Character States is Fixed, SIAM Journal on Computing, vol.23, issue.6, pp.1216-1224, 1994.
DOI : 10.1137/S0097539793244587

A. Amir and D. Keselman, Maximum Agreement Subtree in a Set of Evolutionary Trees: Metrics and Efficient Algorithms, SIAM Journal on Computing, vol.26, issue.6, pp.1656-1669, 1997.
DOI : 10.1137/S0097539794269461

M. Farach, T. M. Przytycka, and M. Thorup, On the agreement of many trees, Information Processing Letters, vol.55, issue.6, pp.297-301, 1995.
DOI : 10.1016/0020-0190(95)00110-X

D. Bryant, Building trees, hunting for trees and comparing trees: theory and method in phylogenetic analysis, 1997.

R. G. Downey, M. R. Fellows, and U. Stege, Computational tractability: The view from mars, Bulletin of the European Association for Theoretical Computer Science, vol.69, pp.73-97, 1999.

V. Berry and F. Nicolas, Improved parametrized complexity of the Maximum Agreement Subtree and Maximum Compatible Tree problems

S. Guillemot and F. Nicolas, Parameterized complexity of the MAST and MCT problems, 2007.

M. Henzinger, V. King, and T. Warnow, Constructing a Tree from Homeomorphic Subtrees, with Applications to Computational Evolutionary Biology, Algorithmica, vol.24, issue.1, pp.1-13, 1999.
DOI : 10.1007/PL00009268

M. Steel and T. Warnow, Kaikoura tree theorems: Computing the maximum agreement subtree, Information Processing Letters, vol.48, issue.2, pp.77-82, 1993.
DOI : 10.1016/0020-0190(93)90181-8

V. Hoang and W. K. Sung, Fixed parameter polynomial time algorithms for maximum agreement and compatible supertrees, Proceedings of STACS'08, pp.361-372, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00227551

H. Bandelt and A. Dress, Reconstructing the shape of a tree from observed dissimilarity data, Advances in Applied Mathematics, vol.7, issue.3, pp.309-343, 1986.
DOI : 10.1016/0196-8858(86)90038-2

H. Fernau, Parameterized Algorithmics: A Graph-Theoretic Approach. Habilitationsschrift, 2005.

J. Gramm and R. Niedermeier, A fixed-parameter algorithm for minimum quartet inconsistency, Journal of Computer and System Sciences, vol.67, issue.4, pp.723-741, 2003.
DOI : 10.1016/S0022-0000(03)00077-1

Y. Chen, J. Flum, and M. Grohe, Bounded nondeterminism and alternation in parameterized complexity theory, 18th IEEE Annual Conference on Computational Complexity, 2003. Proceedings., pp.13-29, 2003.
DOI : 10.1109/CCC.2003.1214407

S. Guillemot, Parameterized Complexity and Approximability of the SLCS Problem, Proceedings of IWPEC'08, pp.115-128, 2008.
DOI : 10.1007/978-3-540-79723-4_12

URL : https://hal.archives-ouvertes.fr/hal-00824929

M. Fellows, M. Hallett, and U. Stege, Analogs & duals of the MAST problem for sequences & trees, Journal of Algorithms, vol.49, issue.1, pp.192-216, 2003.
DOI : 10.1016/S0196-6774(03)00081-6