. Fig, Duplication tree for the 16 genes of human ZNF 45 family inferred by DTSCORE plus LSDT with parsimony; black dots represent the only allowed root positions, according to the tandem duplication model; the (arbitrarily) selected root position is circled. (b) Rooted duplication tree corresponding to tree (a) (c) Phylogeny inferred by TNT. Tree (a) can be obtained from tree (c) by moving ZNF45 and ZNF228 to edge 1, and ZNF233 to edge 2. Edge lengths in tree (a) and tree (c) were estimated by maximum likelihood, Lengths in tree (b) are meaningless and were adjusted to obtain a readable drawing

F. Blattner, G. Plunkett, C. Bloch, N. Perna, V. Burland et al., The Complete Genome Sequence of Escherichia coli K-12, Science, vol.277, issue.5331, pp.1453-1474, 1997.
DOI : 10.1126/science.277.5331.1453

E. Lander, Initial sequencing and analysis of the human genome, Nature, vol.6, issue.6822, pp.860-921, 2001.
DOI : 10.1038/35057062

A. Smit, Interspersed repeats and other mementos of transposable elements in mammalian genomes, Current Opinion in Genetics & Development, vol.9, issue.6, pp.657-663, 1999.
DOI : 10.1016/S0959-437X(99)00031-3

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.

G. Levinson and G. Gutman, Slipped-Strand Mispairing: A Major Mechanism for DNA Sequence Evolution, Molecular Biology and Evolution, vol.4, pp.203-221, 1987.

J. Zhang and M. Nei, Evolution of Antennapedia-Class Homeobox Genes, Genetics, vol.142, issue.1, pp.295-303, 1996.

O. Elemento and O. Gascuel, An Exact and Polynomial Distance- Based Algorithm to Reconstruct Single Copy Tandem Duplication Trees, Proc. 14th Ann. Symp. Combinatorial Pattern Matching (CPM2003), 2003.
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

G. Benson and L. Dong, Reconstructing the Duplication History of a Tandem Repeat, Proc. Intelligent Systems in Molecular Biology (ISMB1999), T. Lengauer, pp.44-53, 1999.

M. Tang, M. Waterman, and S. Yooseph, Zinc Finger Gene Clusters and Tandem Gene Duplication, Journal of Computational Biology, vol.9, issue.2, pp.429-446, 2002.
DOI : 10.1089/10665270252935557

E. Rivals, A SURVEY ON ALGORITHMIC ASPECTS OF TANDEM REPEATS EVOLUTION, International Journal of Foundations of Computer Science, vol.15, issue.02, pp.225-257, 2004.
DOI : 10.1142/S012905410400239X

URL : https://hal.archives-ouvertes.fr/lirmm-00108543

O. Gascuel, D. Bertrand, and O. Elemento, Reconstructing the Duplication History of Tandemly Repeated Sequences, Math. of Evolution and Phylogeny, 2004.
URL : https://hal.archives-ouvertes.fr/lirmm-00106580

S. Ohno, Evolution by Gene Duplication, 1970.
DOI : 10.1007/978-3-642-86659-3

P. L. Fleche, Y. Hauck, L. Onteniente, A. Prieur, F. Denoeud et al., A Tandem Repeats Database for Bacterial Genomes: Application to the Genotyping of Yersinia Pestis and Bacillus Anthracis, BioMed Central Microbiology, vol.1, pp.2-15, 2001.
URL : https://hal.archives-ouvertes.fr/hal-01158341

D. Jaitly, P. Kearney, G. Lin, and B. Ma, 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

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.

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

J. Barthélemy and A. Guénoche, Trees and Proximity Representations, 1991.

S. Sattath and A. Tversky, Additive similarity trees, Psychometrika, vol.42, issue.3, pp.319-345, 1977.
DOI : 10.1007/BF02293654

L. Zhang, B. Ma, L. Wang, and Y. Xu, Greedy method for inferring tandem duplication history, Bioinformatics, vol.19, issue.12, pp.1497-1504, 2003.
DOI : 10.1093/bioinformatics/btg191

D. Swofford and P. *. , Phylogenetic Analysis Using Parsimony (*and Other Methods), version 4, 1999.

J. Felsenstein, PHYLIP?PHYLogeny Inference Package, Cladistics, vol.5, pp.164-166, 1989.

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

D. Robinson, Comparison of labeled trees with valency three, Journal of Combinatorial Theory, Series B, vol.11, issue.2, pp.105-119, 1971.
DOI : 10.1016/0095-8956(71)90020-7

L. Wang and D. Gusfield, Improved Approximation Algorithms for Tree Alignment, Journal of Algorithms, vol.25, issue.2, pp.255-273, 1997.
DOI : 10.1006/jagm.1997.0882

Y. Pauplin, Direct Calculation of a Tree Length Using a Distance Matrix, Journal of Molecular Evolution, vol.51, issue.1, pp.41-47, 2000.
DOI : 10.1007/s002390010065

R. Desper and O. Gascuel, Theoretical Foundation of the Balanced Minimum Evolution Method of Phylogenetic Inference and Its Relationship to Weighted Least-Squares Tree Fitting, Molecular Biology and Evolution, vol.21, issue.3, pp.587-598, 2004.
DOI : 10.1093/molbev/msh049

URL : https://hal.archives-ouvertes.fr/lirmm-00108569

W. Fitch, Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology, Systematic Zoology, vol.20, issue.4, pp.406-416, 1971.
DOI : 10.2307/2412116

J. Hartigan, Minimum Mutation Fits to a Given Tree, Biometrics, vol.29, issue.1, pp.53-65, 1973.
DOI : 10.2307/2529676

G. Ganapathy, V. Ramachandran, and T. Warnow, Better Hill-Climbing Searches for Parsimony, Proc. Third Int, 2003.
DOI : 10.1007/978-3-540-39763-2_19

P. A. Goloboff, METHODS FOR FASTER PARSIMONY ANALYSIS, Cladistics, vol.39, issue.3, pp.199-220, 1996.
DOI : 10.1007/BF01681346

V. Berry and O. Gascuel, Inferring evolutionary trees with strong combinatorial evidence, Theoretical Computer Science, vol.240, issue.2, pp.271-298, 2000.
DOI : 10.1016/S0304-3975(99)00235-2

M. Kimura, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of Molecular Evolution, vol.206, issue.5, Nov., pp.111-120, 1980.
DOI : 10.1007/BF01731581

D. Jones, W. Taylor, and J. Thornton, The rapid generation of mutation data matrices from protein sequences, Bioinformatics, vol.8, issue.3, pp.275-282, 1992.
DOI : 10.1093/bioinformatics/8.3.275

K. Kidd and L. Sgaramella-zonta, Phylogenetic Analysis: Concepts and Methods, Am. J. Human Genetics, vol.23, pp.235-252, 1971.

A. Rzhetsky and M. Nei, Theoretical Foundation of the Minimum-Evolution Method of Phylogenetic Inference, Molecular Biology and Evolution, vol.10, pp.173-1095, 1993.

W. Day, Computational complexity of inferring phylogenies from dissimilarity matrices, Bulletin of Mathematical Biology, vol.42, issue.4, pp.461-467, 1987.
DOI : 10.1007/BF02458863

C. Semple and M. Steel, Cyclic permutations and evolutionary trees, Advances in Applied Mathematics, vol.32, issue.4, pp.669-680, 2004.
DOI : 10.1016/S0196-8858(03)00098-8

R. Desper and O. Gascuel, Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle, Journal of Computational Biology, vol.9, issue.5, pp.687-706, 2002.
DOI : 10.1089/106652702761034136

URL : https://hal.archives-ouvertes.fr/lirmm-00269513

M. Kuhner and J. Felsenstein, A Simulation Comparison of Phylogeny Algorithms under Equal and Unequal Evolutionary Rates, Molecular Biology and Evolution, vol.11, pp.459-468, 1994.

A. Rambault and N. Grassly, Seq-Gen: An Application for the Monte Carlo Simulation of DNA Sequence Evolution Along Phylogenetic Trees, Computer Applied Biosciences, vol.13, pp.235-238, 1997.

J. Felsenstein and G. Churchill, A Hidden Markov Model approach to variation among sites in rate of evolution, Molecular Biology and Evolution, vol.13, issue.1, pp.93-104, 1996.
DOI : 10.1093/oxfordjournals.molbev.a025575

P. A. Goloboff, J. S. Farris, and K. Nixon, TNT: Tree Analysis Using New Technology, 2000.

T. El-barabi and T. Pieler, Zinc Finger Proteins: What We Know and What We Would Like to Know, Mechanisms of Development, vol.33, pp.155-169, 1991.

M. Shannon, J. Kim, L. Ashworth, E. Branscomb, and L. Stubbs, Tandem Zinc-Finger Gene Families in Mammals: Insights and Unanswered Questions, DNA Sequence, vol.16, issue.5, pp.303-315, 1998.
DOI : 10.3109/10425179809034075

P. Waddel and M. Steel, General Time-Reversible Distances with Unequal Rates across Sites: Mixing ?? and Inverse Gaussian Distributions with Invariant Sites, Molecular Phylogenetics and Evolution, vol.8, issue.3, pp.398-414, 1997.
DOI : 10.1006/mpev.1997.0452

K. C. Nixon, The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis, Cladistics, vol.46, issue.4, pp.407-414, 1999.
DOI : 10.1006/clad.1999.0101

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

J. Felsenstein, Cases in which Parsimony or Compatibility Methods Will be Positively Misleading, Systematic Zoology, vol.27, issue.4, pp.401-410, 1978.
DOI : 10.2307/2412923

D. Page and M. Charleston, From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem, Molecular Phylogenetics and Evolution, vol.7, issue.2, pp.231-240, 1997.
DOI : 10.1006/mpev.1996.0390

M. Hallett, J. Lagergren, and A. Tofigh, Simultaneous identification of duplications and lateral transfers, Proceedings of the eighth annual international conference on Computational molecular biology , RECOMB '04, pp.347-356, 2004.
DOI : 10.1145/974614.974660