Reconciling a gene tree to a species tree under the duplication cost model
Theoretical Computer Science
DLS-trees: a model of evolutionary scenarios
Theoretical Computer Science
Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
From Gene Trees to Species Trees through a Supertree Approach
LATA '09 Proceedings of the 3rd International Conference on Language and Automata Theory and Applications
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
Reconciling gene trees to a species tree
CIAC'03 Proceedings of the 5th Italian conference on Algorithms and complexity
Inferring a duplication, speciation and loss history from a gene tree
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
Evolution of tandemly arrayed genes in multiple species
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
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
An efficient method for DNA-based species assignment via gene tree and species tree reconciliation
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Linear-Time Algorithms for the Multiple Gene Duplication Problems
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Simultaneous Identification of Duplications and Lateral Gene Transfers
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Building species trees from larger parts of phylogenomic databases
Information and Computation
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
From Gene Trees to Species Trees II: Species Tree Inference by Minimizing Deep Coalescence Events
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
An improved algorithm for the macro-evolutionary phylogeny problem
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Inferring species phylogenies: a microarray approach
ICIC'06 Proceedings of the 2006 international conference on Computational Intelligence and Bioinformatics - Volume Part III
A hybrid micro-macroevolutionary approach to gene tree reconstruction
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
On the structure of reconciliations
RCG'04 Proceedings of the 2004 RECOMB international conference on Comparative Genomics
Complexity insights of the minimum duplication problem
SOFSEM'12 Proceedings of the 38th international conference on Current Trends in Theory and Practice of Computer Science
Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model
Logic and Program Semantics
GTP supertrees from unrooted gene trees: linear time algorithms for NNI based local searches
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Algorithms for knowledge-enhanced supertrees
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Minimum leaf removal for reconciliation: complexity and algorithms
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
An optimal reconciliation algorithm for gene trees with polytomies
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Accounting for gene tree uncertainties improves gene trees and reconciliation inference
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Unrooted Tree Reconciliation: A Unified Approach
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Efficient Algorithms for Knowledge-Enhanced Supertree and Supermatrix Phylogenetic Problems
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Gene tree correction for reconciliation and species tree inference: Complexity and algorithms
Journal of Discrete Algorithms
Hi-index | 0.00 |
This paper studies various algorithmic issues in reconstructing a species tree from gene trees under the duplication and the mutation cost model. This is a fundamental problem in computational molecular biology. Our main results are as follows. A linear time algorithm is presented for computing all the losses in duplications associated with the least common ancestor mapping from a gene tree to a species tree. This answers a problem raised recently by Eulenstein, Mirkin, and Vingron [J. Comput. Bio., 5 (1998), pp. 135--148]. The complexity of finding an optimal species tree from gene trees is studied. The problem is proved to be NP-hard for the duplication cost and for the mutation cost. Further, the concept of reconciled trees was introduced by Goodman et al. and formalized by Page for visualizing the relationship between gene and species trees. We show that constructing an optimal reconciled tree for gene trees is also NP-hard. Finally, we consider a general reconstruction problem and show it to be NP-hard even for the well-known nearest neighbor interchange distance. A new and efficiently computable metric is defined based on the duplication cost. We show that the problem of finding an optimal species tree from gene trees is NP-hard under this new metric but it can be approximated within factor 2 in polynomial time. Using this approximation result, we propose a heuristic method for finding a species tree from gene trees with uniquely labeled leaves under the duplication cost. Our experimental tests demonstrate that when the number of species is larger than 15 and gene trees are close to each other, our heuristic method is significantly better than the existing program in Page's GeneTree 1.0 that starts the search from a random tree.