Algorithms for Reticulate Networks of Multiple Phylogenetic Trees

Close lower and upper bounds for the minimum reticulate network of multiple phylogenetic trees

MOTIVATION Reticulate network is a model for displaying and quantifying the effects of complex reticulate processes on the evolutionary history of species undergoing reticulate evolution. A central computational problem on reticulate networks is: given a set of phylogenetic trees (each for some region of the genomes), reconstruct the most parsimonious reticulate network (called the minimum reti...

Reconstruction of Reticulate Networks from Gene Trees

One of the simplest evolutionary models has molecular sequences evolving from a common ancestor down a bifurcating phylogenetic tree, experiencing point-mutations along the way. However, empirical analyses of different genes indicate that the evolution of genomes is often more complex than can be represented by such a model. Thus, the following problem is of significant interest in molecular ev...

Algorithms on Phylogenetic Trees

Supplemental materials for “Close Lower and Upper Bounds for the Minimum Reticulate Network of Multiple Phylogenetic Trees”

Recall that non-binary nodes in N are nodes with out-degrees of three or more. Nodes with outdegrees of two are called binary nodes. Here, we describe some subtle issues on networks with non-binary nodes. Note that a non-binary node indicates uncertainty in branching order at this node. Only binary nodes exist in the “true” network: it is considered to be very unlikely to have two speciation ev...

Algorithms for Visualizing Phylogenetic Networks

We study the problem of visualizing phylogenetic networks, which are extensions of the Tree of Life in biology. We use a space filling visualization method, called DAGmaps, in order to obtain clear visualizations using limited space. In this paper, we restrict our attention to galled trees and galled networks and present linear time algorithms for visualizing them as DAGmaps.