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ISIPhyNC

Welcome to ISIPhyNC, the Information System on Inclusions of Phylogenetic Network Classes, which provides information about subclasses of phylogenetic networks.


This website focuses only on rooted explicit phylogenetic networks, that is directed acyclic graphs with a root (a vertex of indegree 0) and leaves (vertices with outdegree 0) which are usually labeled by distinct labels corresponding to biological taxa.

Classes of explicit phylogenetic networks

Classes of binary networks

An arrow from class A to class B means that A contains B (another version of this graph, drawn with GraphViz, is available here).
To have more information about the subclasses and the proofs of inclusion, please follow the links in the list of subclasses below.
G binary galled tree binary galled tree binary phylogenetic tree binary phylogenetic tree binary galled tree->binary phylogenetic tree binary unicyclic binary unicyclic binary galled tree->binary unicyclic binary normal binary normal binary normal->binary phylogenetic tree binary leaf outerplanar binary leaf outerplanar binary leaf outerplanar->binary galled tree binary spread-1 binary spread-1 binary spread-1->binary leaf outerplanar binary spread-2 binary spread-2 binary spread-2->binary spread-1 binary level-2 binary level-2 binary spread-2->binary level-2 binary spread-3 binary spread-3 binary spread-3->binary spread-2 binary level-3 binary level-3 binary spread-3->binary level-3 binary spread-k binary spread-k binary spread-k->binary spread-3 binary level-k binary level-k binary spread-k->binary level-k binary binary binary->binary spread-k binary tree-based binary tree-based binary->binary tree-based binary nearly stable binary nearly stable binary->binary nearly stable binary time-consistent binary time-consistent binary->binary time-consistent binary k-reticulated binary k-reticulated binary->binary k-reticulated binary stable-child binary stable-child binary->binary stable-child binary level-2->binary galled tree binary level-3->binary level-2 binary level-k->binary level-3 binary tree-based->binary level-2 binary compressed binary compressed binary tree-based->binary compressed binary tree-sibling binary tree-sibling binary tree-based->binary tree-sibling binary reticulation-visible binary reticulation-visible binary compressed->binary reticulation-visible binary FU-stable binary FU-stable binary compressed->binary FU-stable binary 2-nested binary 2-nested binary 2-nested->binary galled tree binary 3-nested binary 3-nested binary 3-nested->binary 2-nested binary k-nested binary k-nested binary k-nested->binary 3-nested binary nested binary nested binary nested->binary k-nested binary 1-reticulated binary 1-reticulated binary 1-reticulated->binary nested binary nearly tree-child binary nearly tree-child binary tree-child binary tree-child binary nearly tree-child->binary tree-child binary tree-child->binary galled tree binary tree-child->binary normal binary genetically stable binary genetically stable binary genetically stable->binary nearly tree-child binary reticulation-visible->binary genetically stable binary galled network binary galled network binary reticulation-visible->binary galled network binary nearly stable->binary tree-child binary tree-sibling->binary genetically stable binary regular binary regular binary regular->binary normal binary distinct-cluster binary distinct-cluster binary distinct-cluster->binary regular binary FU-stable->binary genetically stable binary FU-stable->binary distinct-cluster binary galled network->binary galled tree binary time-consistent->binary phylogenetic tree binary 2-reticulated binary 2-reticulated binary 2-reticulated->binary level-2 binary 2-reticulated->binary 1-reticulated binary 3-reticulated binary 3-reticulated binary 3-reticulated->binary level-3 binary 3-reticulated->binary 2-reticulated binary k-reticulated->binary level-k binary k-reticulated->binary 3-reticulated binary stable-child->binary tree-child

List of classes:

Classes with unbounded degree

List of classes:

Problems and properties studied on these classes

Problems

Properties

Examples of networks in these classes

About this website

This website was programmed and is maintained by Philippe Gambette. It was started during the internship of Maxime Morgado at LIGM, in June-July 2015, and also contains contributions made from Narges Tavassoli from November 2016 to January 2017.

Please contact Philippe Gambette if you have any suggestions about this website, especially about problems, properties, results or subclasses to add.

How to cite

P. Gambette, M. Morgado & N. Tavassoli (2017) ISIPhyNC, an Information System on Inclusions of Phylogenetic Network Classes, manuscript in preparation.

Database content

73 classes of phylogenetic networks including 35 classes of binary phylogenetic networks (defined in a total of 20 bibliographic references), 51 inclusion relationships proved directly between classes (including some found in a total of 9 bibliographic references), 24 networks (68 memberships to a class, 56 non-memberships to a class), 3 problems considered, 3 properties considered, 33 theorems proved directly (including some found in a total of 15 bibliographic references) including 23 positive results (which can be extended to subclasses) and 10 negative results (which can be extended to superclasses).

 

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