The binary perfect phylogeny with persistent characters
@article{Bonizzoni2011TheBP, title={The binary perfect phylogeny with persistent characters}, author={Paola Bonizzoni and Chiara Braghin and Riccardo Dondi and Gabriella Trucco}, journal={Theor. Comput. Sci.}, year={2011}, volume={454}, pages={51-63} }
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Algorithms for the Constrained Perfect Phylogeny with Persistent Characters
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An integer programming solution to the Persistent-Phylogeny Problem is developed; empirically explore its efficiency; and the utility of using fast algorithms that recognize galled trees, to recognize persistent phylogeny is explored.
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A distance metric for multi-labeled trees is presented that generalizes the Robinson-Foulds distance for phylogenetic trees, allows for a similarity assessment at much higher resolution, and can be applied to trees and networks with different sets of node labels.
References
SHOWING 1-10 OF 22 REFERENCES
Incomplete Directed Perfect Phylogeny
- BiologyCPM
- 2000
This work provides a near optimal O(nm)-time algorithm for the problem of perfect phylogeny, which arises in classical phylogenetic studies, when some states are missing or undetermined.
Reducing Multi-state to Binary Perfect Phylogeny with Applications to Missing, Removable, Inserted, and Deleted Data
- Computer ScienceWABI
- 2010
A new general conceptual solution to the multistate Perfect Phylogeny problem is introduced, and conceptual solutions to the MD, CR, MDCR and ID problems for any k significantly improving previous work are introduced.
Algorithms for Efficient Near-Perfect Phylogenetic Tree Reconstruction in Theory and Practice
- Computer ScienceIEEE/ACM Transactions on Computational Biology and Bioinformatics
- 2007
This work proves that the BNPP problem is fixed-parameter tractable and provides the first practical phylogenetic tree reconstruction algorithms that find guaranteed optimal solutions while being easily implemented and computationally feasible for data sets of biologically meaningful size and complexity.
The Perfect Phylogeny Problem
- Biology
- 2001
This work is concerned here with taxa described by the states they exhibit on a set of characters, and assumes that the taxa descend from a common ancestor where all characters are absent.
Constructing Near-Perfect Phylogenies with multiple homoplasy events
- Computer ScienceISMB
- 2006
A near-optimal algorithm is presented for the H1-NPPH problem, which is to determine if a given set of genotypes admit a phylogeny with a single homoplasy event, and the accuracy of this algorithm is comparable to that of the existing methods, while being orders of magnitude faster.
An Optimal Algorithm for Perfect Phylogeny Haplotyping
- Computer ScienceJ. Comput. Biol.
- 2006
The OPPH algorithm is one of the first O(nm) algorithms presented for the PPH problem and the FlexTree (flexible tree) data structure provides a compact representation of all the perfect phylogenies for the given set of genotypes.
A Linear-Time Algorithm for the Perfect Phylogeny Haplotype Problem
- Computer Science, MathematicsAlgorithmica
- 2007
The Perfect Phylogeny Haplotype problem is solved and an O(nm)-time algorithm to complete matrices of n rows and m columns to represent PPH solutions is given: it is shown that solving the problem requires recognizing special posets of width 2.
Extensions and Improvements to the Chordal Graph Approach to the Multistate Perfect Phylogeny Problem
- MathematicsIEEE/ACM Transactions on Computational Biology and Bioinformatics
- 2011
This work shows how to use chordal graphs and triangulations to solve the character removal problem for an arbitrary number of states, which was previously unsolved, and outlines a preprocessing technique that speeds up the computation of the minimal separators of a graph.
Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
- Computer ScienceRECOMB '02
- 2002
This paper explores the algorithmic implications of the key "no-recombination in long blocks" observation, for the problem of inferring haplotypes in populations, and observes that the no-re Combination assumption is very powerful.
Efficient reconstruction of haplotype structure via perfect phylogeny.
- BiologyJournal of bioinformatics and computational biology
- 2003
A simple and efficient polynomial-time algorithm for inferring haplotypes from the genotypes of a set of individuals assuming a perfect phylogeny is presented and a hardness result for the problem of removing the minimum number of individuals from a population is presented to ensure that the genotype of the remaining individuals are consistent with aperfect phylogeny.