# 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}
}
• Published 31 October 2011
• Computer Science
• Theor. Comput. Sci.

## Tables from this paper

• Computer Science
ArXiv
• 2014
This paper develops a parameterized algorithm for solving the Persistent Perfect Phylogeny problem where the parameter is the number of characters and provides a polynomial time solution for the CP-PP problem for matrices having an empty conflict-graph.
• Computer Science
• 2021
Insight into the specific structure of the IDPP problem leads to an asymptotically faster algorithm, that runs in optimal $O(nm)$ time, and is successful in giving a much simpler $\tilde{O}( nm)$-time algorithm.
• Biology
BCB
• 2017
An experimental analysis shows that the ILP approach is able to explain data that do not fit the perfect phylogeny assumption, thereby allowing multiple losses and gains of mutations, and a number of subpopulations that is smaller than the number of input mutations.
• 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.
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.
• Biology
bioRxiv
• 2017
This work proposes a new approach that incorporates the possibility of losing a previously acquired mutation, extending the Persistent Phylogeny model, and exploits the model to provide an ILP formulation of the problem of reconstructing trees on mixed populations, where the input data consists of the fraction of cells in a set of samples that have a certain mutation.
• Biology, Computer Science
BCB
• 2020
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

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