7 research outputs found
The class of algebraically closed p-semilattices is finitely axiomatizable
We prove our title, and thereby establish the base for a positive solution of Albert and Burris' problem on the finite axiomatizability of the model companion of the class of all pseudocomplemented semilattice
Computing galled networks from real data
Motivation: Developing methods for computing phylogenetic networks from biological data is an important problem posed by molecular evolution and much work is currently being undertaken in this area. Although promising approaches exist, there are no tools available that biologists could easily and routinely use to compute rooted phylogenetic networks on real datasets containing tens or hundreds of taxa. Biologists are interested in clades, i.e. groups of monophyletic taxa, and these are usually represented by clusters in a rooted phylogenetic tree. The problem of computing an optimal rooted phylogenetic network from a set of clusters, is hard, in general. Indeed, even the problem of just determining whether a given network contains a given cluster is hard. Hence, some researchers have focused on topologically restricted classes of networks, such as galled trees and level-k networks, that are more tractable, but have the practical draw-back that a given set of clusters will usually not possess such a representation
Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters
Phylogenetic trees are widely used to display estimates of how groups of
species evolved. Each phylogenetic tree can be seen as a collection of
clusters, subgroups of the species that evolved from a common ancestor. When
phylogenetic trees are obtained for several data sets (e.g. for different
genes), then their clusters are often contradicting. Consequently, the set of
all clusters of such a data set cannot be combined into a single phylogenetic
tree. Phylogenetic networks are a generalization of phylogenetic trees that can
be used to display more complex evolutionary histories, including reticulate
events such as hybridizations, recombinations and horizontal gene transfers.
Here we present the new CASS algorithm that can combine any set of clusters
into a phylogenetic network. We show that the networks constructed by CASS are
usually simpler than networks constructed by other available methods. Moreover,
we show that CASS is guaranteed to produce a network with at most two
reticulations per biconnected component, whenever such a network exists. We
have implemented CASS and integrated it in the freely available Dendroscope
software
Dendroscope: An interactive viewer for large phylogenetic trees
<p>Abstract</p> <p>Background</p> <p>Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desirable to have a program that provides these services in an effcient and user-friendly way, and that can be easily installed and run on all major operating systems. Although a large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. Moreover, many programs are diffcult to install or are not available for all common operating systems.</p> <p>Results</p> <p>We have developed a new program, Dendroscope, for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool. The software is written in Java 1.4 and installers are provided for Linux/Unix, MacOS X and Windows XP.</p> <p>Conclusion</p> <p>Dendroscope is a user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets.</p