Solving the Persistent Phylogeny Problem in polynomial time
@article{Bonizzoni2016SolvingTP, title={Solving the Persistent Phylogeny Problem in polynomial time}, author={Paola Bonizzoni and Gianluca Della Vedova and Gabriella Trucco}, journal={ArXiv}, year={2016}, volume={abs/1611.01017} }
The notion of a Persistent Phylogeny generalizes the well-known Perfect phylogeny model that has been thoroughly investigated and is used to explain a wide range of evolutionary phenomena. More precisely, while the Perfect Phylogeny model allows each character to be acquired once in the entire evolutionary history while character losses are not allowed, the Persistent Phylogeny model allows each character to be both acquired and lost exactly once in the evolutionary history. The Persistent…
6 Citations
Combinatorial views on persistent characters in phylogenetics
- BiologyAdv. Appl. Math.
- 2020
PE ] 2 1 M ar 2 01 9 Combinatorial views on persistent characters in phylogenetics
- Biology
- 2019
The question of how many binary characters together with their persistence status are needed to uniquely determine a phylogenetic tree is considered and an upper bound for the number of characters needed is provided.
PE ] 1 1 O ct 2 01 8 Combinatorial views on persistent characters in phylogenetics
- Biology
- 2018
The question of how many binary characters together with their persistence status are needed to uniquely determine a phylogenetic tree is considered and an upper bound for the number of characters needed is provided.
Combinatorial perspectives on Dollo-k characters in phylogenetics
- Computer ScienceAdv. Appl. Math.
- 2021
Having an Insight into Malware Phylogeny: Building Persistent Phylogeny Tree of Families
- Computer ScienceIEICE Trans. Inf. Syst.
- 2018
A novel malware phylogeny construction method taking advantage of persistent phylogeny tree model, whose nodes correspond to input instances and edges represent the gain or lost of functional characters is proposed.
Character-Based Phylogeny Construction and Its Application to Tumor Evolution
- BiologyCiE
- 2017
Character-based Phylogeny Construction is a well-known combinatorial problem whose input is a matrix M and we want to compute a phylogeny that is compatible with the actual species encoded by M.
References
SHOWING 1-10 OF 33 REFERENCES
Persistent phylogeny: a galled-tree and integer linear programming approach
- BiologyBCB
- 2015
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.
Explaining evolution via constrained persistent perfect phylogeny
- BiologyBMC Genomics
- 2014
This paper investigates the computational problem of explaining binary data by the Persistent Perfect Phylogeny model (referred as PPP) and investigates the problem of reconstructing an evolution where some constraints are imposed on the paths of the tree.
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.
A colored graph approach to perfect phylogeny with persistent characters
- MathematicsTheor. Comput. Sci.
- 2017
A fast algorithm for the computation and enumeration of perfect phylogenies when the number of character states is fixed
- Computer ScienceSODA '95
- 1995
It is shown how it is possible to efficiently build a structure that implicitly represents the set of all perfect phylogenies and to randomly sample from that set.
Two Strikes Against Perfect Phylogeny
- MathematicsICALP
- 1992
It is shown that the general problem of computation of phytogenies for species sets is NP-Complete, and that the various finite-state approaches for bounded treewidth cannot be applied to the fixed-parameter forms of the problem.
Minimizing Phylogenetic Number To Find Good Evolutionary Trees
- BiologyDiscret. Appl. Math.
- 1996
When and How the Perfect Phylogeny Model Explains Evolution
- BiologyDiscrete and Topological Models in Molecular Biology
- 2014
It is shown that, in this setting, some graph-theoretical notions can provide a characterization of the relationships between characters, playing a crucial role in developing algorithmic solutions to the problem of reconstructing a maximum parsimony tree.
A polynomial-time algorithm for the perfect phylogeny problem when the number of character states is fixed
- Computer ScienceProceedings of 1993 IEEE 34th Annual Foundations of Computer Science
- 1993
We present a polynomial-time algorithm for determining whether a set of species, described by the characters they exhibit, has a perfect phylogeny, assuming the maximum number of possible states for…