Quartets and Unrooted phylogenetic Networks
This article introduces the unrooted analog of level-k networks, a special kind of abstract network to visualize conflicts between phylogenetic trees which may correspond to such exchanges, and gives an equivalence theorem between circular split systems and un rooted level-1 networks.
Computing galled networks from real data
It is argued that galled networks (a generalization of galled trees) provide a good trade-off between level of generality and tractability and solve the problem of computing an optimal rooted phylogenetic network from a set of clusters.
Visualising a Text with a Tree Cloud
A new visualisation which displays more information: the tree cloud, which shows the most frequent words of the text, where the size reflects the frequency, but the words are arranged on a tree to reflect their semantic proximity according to the text.
The Structure of Level-k Phylogenetic Networks
The structure oflevel-k networks, and how they can be decomposed into level-k generators, is studied, and a polynomial time algorithm is provided which takes as input the set of level- k generators and builds theSet of level-(k + 1) generators.
On encodings of phylogenetic networks of bounded level
Phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees, such networks canonically induce collections of phylogenetic trees,…
Normalisation of 16th and 17th century texts in French and geographical named entity recognition
The results show that manual normalisation leads to better results for all methods and that automatic normalisation performs differently depending on the tool used to extract geographical named entities, but with a significant improvement on most methods.
Rearrangement moves on rooted phylogenetic networks
- Philippe Gambette, L. Iersel, Mark Jones, Manuel Lafond, F. Pardi, Céline Scornavacca
- BiologyPLoS Comput. Biol.
- 1 August 2017
This paper proposes “horizontal” moves that ensure that every network of a certain complexity can be reached from any other network of the same complexity, and “vertical” Moves that ensure reachability between networks of different complexities that are robust to the fact that networks with higher complexity usually allow a better fit with the data.
Clust&See: A Cytoscape plugin for the identification, visualization and manipulation of network clusters
Locating a Tree in a Phylogenetic Network in Quadratic Time
- Philippe Gambette, Andreas D. M. Gunawan, A. Labarre, Stéphane Vialette, Louxin Zhang
- BiologyAnnual International Conference on Research in…
- 11 February 2015
A quadratic-time algorithm for this problem for binary nearly-stable phylogenetic networks is developed and it is shown that the number of reticulations in a reticulation visible or nearly stable phylogenetic network is bounded from above by a function linear in theNumber of taxa.
Improved Layout of Phylogenetic Networks
- Philippe Gambette, D. Huson
- Computer ScienceIEEE/ACM Transactions on Computational Biology…
- 1 July 2008
An algorithm for maximizing the area covered by the network is presented, an extension of the equal-daylight algorithm to networks is described, and an investigation into using a spring embedder is looked into.