Dendroscope 3 is a new program for working with rooted phylogenetic trees and networks. It provides a number of methods for drawing and comparing rooted phylogenetic networks, and for computing them from rooted trees. The program can be used interactively or in command-line mode. The program is written in Java, use of the software is free, and installers for all 3 major operating systems can be downloaded from www.dendroscope.org. [Phylogenetic trees; phylogenetic networks; software.].

https://hal.archives-ouvertes.fr/hal-02154987/document

Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks.

The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at www.phylogenetic-networks.org.

Phylogenetic Networks: Concepts, Algorithms and Applications

The evolutionary history of a set of species is usually described by a rooted phylogenetic tree Although it is generally undisputed that bifurcating speciation events and descent with modifications are major forces of evolution, there is a growing belief that reticulate events also have a role to play Phylogenetic networks provide an alternative to phylogenetic trees and may be more suitable for data sets where evolution involves significant amounts of reticulate events, such as hybridization, horizontal gene transfer, or recombination In this article, we give an introduction to the topic of phylogenetic networks, very briefly describing the fundamental concepts and summarizing some of the most important combinatorial methods that are available for their computation

https://hal.archives-ouvertes.fr/hal-02155011/document

A Survey of Combinatorial Methods for Phylogenetic Networks

This paper considers the problem of determining whether a given set $\T$ of rooted triplets can be merged without conflicts into a galled phylogenetic network and, if so, constructing such a network. When the input $\T$ is dense, we solve the problem in $O(|\T|)$ time, which is optimal since the size of the input is $\Theta(|\T|)$. In comparison, the previously fastest algorithm for this problem runs in $O(|\T|^2)$ time. We also develop an optimal $O(|\T|)$-time algorithm for enumerating all simple phylogenetic networks leaf-labeled by $L$ that are consistent with $\T$, where $L$ is the set of leaf labels in $\T$, which is used by our main algorithm. Next, we prove that the problem becomes NP-hard if extended to nondense inputs, even for the special case of simple phylogenetic networks. We also show that for every positive integer $n$, there exists some set $\T$ of rooted triplets on $n$ leaves such that any galled network can be consistent with at most $0.4883 \cdot |\T|$ of the rooted triplets in $\T$. On the other hand, we provide a polynomial-time approximation algorithm that always outputs a galled network consistent with at least a factor of $\frac{5}{12}$ ($> 0.4166$) of the rooted triplets in $\T$.

/pdf/algorithms-for-combining-rooted-triplets-into-a-galled-1qldp1dzdv.pdf

Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network

https://dflund.se/~jj/Publications/ipnrt8_TCS2006.pdf

Inferring a level-1 phylogenetic network from a dense set of rooted triplets

https://dflund.se/~jj/Publications/masn8_TCS2005.pdf

Computing the maximum agreement of phylogenetic networks

We introduce the maximum agreement phylogenetic subnetwork problem (MASN) of finding a branching structure shared by a set of phylogenetic networks. We prove that the problem is NP-hard even if restricted to three phylogenetic networks and give an O(n2)-time algorithm for the special case of two level-1 phylogenetic networks, where n is the number of leaves in the input networks and where N is called a level-f phylogenetic network if every biconnected component in the underlying undirected graph contains at most f nodes having indegree 2 in N. Our algorithm can be extended to yield a polynomial-time algorithm for two level-f phylogenetic networks N1,N2 for any f which is upper-bounded by a constant; more precisely, its running time is O(|V(N1)|·|V(N2)|·4f), where V(Ni) denotes the set of nodes of Ni.

Charles Choy

Papers

Computing the maximum agreement of phylogenetic networks

Computing the Maximum Agreement of Phylogenetic Networks