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PRODORIC: prokaryotic database of gene regulation
The database PRODORIC aims to systematically organize information on prokaryotic gene expression, and to integrate this information into regulatory networks. The present version focuses on pathogenic…
A Reduction Algorithm for Computing The Hybridization Number of Two Trees
- M. Bordewich, S. Linz, Katherine St John, C. Semple
- Computer ScienceEvolutionary bioinformatics online
- 30 May 2007
A new reduction-based algorithm for computing the minimum number of hybridization events, when the initial data set consists of two trees, which always gives the exact solution and runs efficiently on many real biological problems.
Hybridization in Non-Binary Trees
The NP-hard problem of calculating the minimum number of reticulation events for two (arbitrary) rooted phylogenetic trees parameterized by this minimum number is fixed-parameter tractable.
Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks.
A Cluster Reduction for Computing the Subtree Distance Between Phylogenies
A divide-and-conquer approach to calculating the rSPR distance is established that breaks the problem instance into a number of smaller and more tractable subproblems and shows that this distance is fixed-parameter tractable.
Hybridization in Nonbinary Trees
It is shown that the NP-hard problem of calculating the minimum number of reticulation events for two (arbitrary) rooted phylogenetic trees parameterized by this minimum number is fixed-parameter tractable.
A quadratic kernel for computing the hybridization number of multiple trees
Cherry Picking: A Characterization of the Temporal Hybridization Number for a Set of Phylogenies
The first characterization of the problem for the minimum–temporal-hybridization number for a set of rooted binary phylogenetic trees being arbitrarily large is given, in terms of cherries and the existence of a particular type of sequence.
Attaching leaves and picking cherries to characterise the hybridisation number for a set of phylogenies
Quantifying Hybridization in Realistic Time
A new fixed-parameter algorithm for computing the minimum number of hybridization events for when two rooted binary phylogenetic trees are given is given, based on interleaving-a technique using repeated kernelization steps that are applied throughout the exhaustive search part of a fixed- parameter algorithm.