G. Benson and L. Dong, Reconstructing the duplication history of a tandem repeat, Proceedings of Intelligent Systems in Molecular Biology (ISMB1999), pp.44-53, 1999.

D. Bertrand and O. Gascuel, Topological rearrangements and local search method for tandem duplication trees, IEEE Transactions on Computational Biology and Bioinformatics, pp.15-28, 2005.
URL : https://hal.archives-ouvertes.fr/lirmm-00105315

K. Chen, D. Durand, and M. Farach-colton, Notung, Proceedings of the fourth annual international conference on Computational molecular biology , RECOMB '00, 2000.
DOI : 10.1145/332306.332351

N. El-mabrouk, Genome Rearrangement by Reversals and Insertions/Deletions of Contiguous Segments, CPM 2000, pp.222-234, 2000.
DOI : 10.1007/3-540-45123-4_20

O. Elemento and O. Gascuel, An efficient and accurate distance based algorithm to reconstruct tandem duplication trees, Bioinformatics, vol.18, issue.Suppl 2, pp.92-99, 2002.
DOI : 10.1093/bioinformatics/18.suppl_2.S92

O. Elemento and O. Gascuel, An exact and polynomial distance-based algorithm to reconstruct single copy tandem duplication trees, Journal of Discrete Algorithms, vol.2, pp.362-374, 2005.
URL : https://hal.archives-ouvertes.fr/lirmm-00105291

O. Elemento, O. Gascuel, and M. Lefranc, Reconstructing the Duplication History of Tandemly Repeated Genes, Molecular Biology and Evolution, vol.19, issue.3, pp.278-288, 2002.
DOI : 10.1093/oxfordjournals.molbev.a004081

URL : https://hal.archives-ouvertes.fr/lirmm-00268603

F. Ronquist and J. H. , MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, vol.19, issue.12, pp.1572-1576, 2003.
DOI : 10.1093/bioinformatics/btg180

W. Fitch, Phylogenies constrained by cross-over process as illustrated by human hemoglobins in a thirteen-cycle, eleven amino-acid repeat in human apolipoprotein A-I, Genetics, vol.86, pp.623-644, 1977.

O. Gascuel, D. Bertrand, and O. Elemento, Reconstructing the duplication history of tandemly repeated sequences, Mathematics of Evolution and Phylogeny, pp.205-235, 2005.
URL : https://hal.archives-ouvertes.fr/lirmm-00106580

O. Gascuel, M. Hendy, A. Jean-marie, and S. Mclachlan, The Combinatorics of Tandem Duplication Trees, Systematic Biology, vol.52, issue.1, pp.110-118, 2003.
DOI : 10.1080/10635150390132821

URL : https://hal.archives-ouvertes.fr/lirmm-00192006

G. Glusman, I. Yanai, I. Rubin, and D. Lancet, The Complete Human Olfactory Subgenome, Genome Research, vol.11, issue.5, pp.685-702, 2001.
DOI : 10.1101/gr.171001

R. Guigó, I. Muchnik, and T. Smith, Reconstruction of Ancient Molecular Phylogeny, Molecular Phylogenetics and Evolution, vol.6, issue.2, pp.189-213, 1996.
DOI : 10.1006/mpev.1996.0071

A. Hamilton, S. Huntley, M. Tran-gyamfi, D. Baggott, L. Gordon et al., Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes, Genome Research, vol.16, issue.5, pp.584-594, 2006.
DOI : 10.1101/gr.4843906

S. Hannenhalli and P. A. Pevzner, Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals, Journal of the ACM, vol.46, issue.1, pp.1-27, 1999.
DOI : 10.1145/300515.300516

S. Huntley, D. Baggot, A. Hamilton, M. Trangyamfi, S. Y. Kim et al., A comprehensive catalog of human KRAB-associated zinc finger genes: Insights into the evolutionary history of a large family of transcriptional repressors, Genome Research, vol.16, issue.5, pp.669-677, 2006.
DOI : 10.1101/gr.4842106

D. Jaitly, P. Kearney, G. Lin, M. , and B. , Methods for reconstructing the history of tandem repeats and their application to the human genome, Journal of Computer and System Sciences, vol.65, issue.3, pp.494-507, 2002.
DOI : 10.1016/S0022-0000(02)00006-5

H. Kaplan, R. Shamir, and R. E. Tarjan, A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals, SIAM Journal on Computing, vol.29, issue.3, pp.880-892, 2000.
DOI : 10.1137/S0097539798334207

C. Lanave, G. Preparata, C. Saccone, and G. Serio, A new method for calculating evolutionary substitution rates, Journal of Molecular Evolution, vol.46, issue.1, pp.86-93, 1984.
DOI : 10.1007/BF02101990

B. Ma, M. Li, and L. Zhang, On reconstructing species trees from gene trees in term of duplications and losses, Proceedings of the second annual international conference on Computational molecular biology , RECOMB '98, pp.182-191, 1998.
DOI : 10.1145/279069.279113

R. Page and M. Charleston, Reconciled trees and incongruent gene and species trees, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol.37, pp.57-70, 1997.

J. Robinson, M. Waller, P. Parham, N. De-groot, R. Bontrop et al., IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex, Nucleic Acids Research, vol.31, issue.1, pp.311-315, 2003.
DOI : 10.1093/nar/gkg070

M. Ruiz, V. Giudicelli, C. Ginestoux, P. Stoehr, J. Robinson et al., IMGT, the international ImMunoGeneTics database, IMGT, the international ImMunoGeneTics database, pp.219-221, 2000.
DOI : 10.1093/nar/28.1.219

N. Saitou and M. Nei, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Molecular Biology and Evolution, vol.4, pp.406-425, 1987.

M. Shannon, A. Hamilton, L. Gordon, E. Branscomb, and L. Stubbs, Differential Expansion of Zinc-Finger Transcription Factor Loci in Homologous Human and Mouse Gene Clusters, Genome Research, vol.13, issue.6, pp.1097-1110, 2003.
DOI : 10.1101/gr.963903