Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
From Gene Trees to Species Trees
SIAM Journal on Computing
Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
An Ω(n^2/ log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
The gene-duplication problem: near-linear time algorithms for NNI based local searches
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
Natural Computing: an international journal
H-trees: a Model of Evolutionary Scenarios with Horizontal Gene Transfer
Fundamenta Informaticae - From Mathematical Beauty to the Truth of Nature: to Jerzy Tiuryn on his 60th Birthday
A linear time algorithm for error-corrected reconciliation of unrooted gene trees
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
Removing noise from gene trees
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model
Logic and Program Semantics
Minimum leaf removal for reconciliation: complexity and algorithms
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
RECOMB'13 Proceedings of the 17th international conference on Research in Computational Molecular Biology
Gene tree correction for reconciliation and species tree inference: Complexity and algorithms
Journal of Discrete Algorithms
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The general problem of reconciling the information from evolutionary trees representing the relationships between distinct gene families is of great importance in bioinformatics and has been popularized among the computer science researchers by Ma et al. [From gene trees to species trees, SIAM J. Comput. 30(3) (2000) 729-752] where the authors pose the intriguing question if a certain definition of minimum tree that reconciles a gene tree and a species tree is correct. We answer affirmatively to this question; moreover, we show an efficient algorithm for computing such minimum-leaf reconciliation trees and prove the uniqueness of such trees. We then tackle some different versions of the biological problem by showing that the exemplar problem, arising from the exemplar analysis of multigene genomes, is NP-hard even when the number of copies of a given label is at most two. Finally, we introduce two novel formulations for the problem of recombining evolutionary trees, extending the gene duplication problem studied in [Ma et al., From gene trees to species trees, SIAM J. Comput. 30(3) (2000) 729-752; M. Fellows et al., On the multiple gene duplication problem, in: Proc. Ninth Internat. Symp. on Algorithms and Computation (ISAAC98), 1998; R. Page, Maps between trees and cladistic analysis of historical associations among genes, Systematic Biology 43 (1994) 58-77; R.M. Page, J. Cotton, Vertebrate phylogenomics: reconciled trees and gene duplications, in: Proc. Pacific Symp. on Biocomputing 2002 (PSB2002), 2002, pp. 536-547; R. Guigò et al., Reconstruction of ancient molecular phylogeny, Mol. Phy. and Evol. 6(2) (1996) 189-213], and we give an exact algorithm (via dynamic programming) for one of these formulations.