Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation non-treelike evolutionary events such as hybridization. Typically, have been analyzed based on their ‘level’, i.e. complexity 2-edge-connected components. However, recently question how ‘treelike’ network is has become center attention in various studies. This led to introduction tree-based networks...

Several artificial organisms are shown on the cards. These drawings have been prepared so that it is easy to find differences and to distinguish between the characteristics of each organism. No numerical data are needed to distinguish between characteristics such as long and short birds’ tails. In contrast, with real organisms a researcher must usually collect numerical data and subjectively de...

1 Tutorial Summary All biological disciplines are united by the idea that species share a common history. The genealogical history of life-also called an \evolutionary tree"-is usually represented by a bifurcating, leaf-labeled tree. The use of evolutionary trees is a fundamental step in many biological problems, such as multiple sequence alignments, protein structure and function prediction, a...

MOTIVATION Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a reconciliation of minimum total cost. It is...

The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cel...

Evolutionary relationships among species are usually (i) illustrated by means of a phylogenetic tree and (ii) inferred by optimising some measure of fitness, such as the total evolutionary distance between species or the likelihood of the tree (given a model of the evolutionary process and a data set). The combinatorial complexity of inferring the topology of the best tree makes phylogenetic in...

Phylogenetic tree construction process might produce many candidate trees as the "best estimates." As the number of constructed phylogenetic trees grows, the need to efficiently compare their topological or physical structures arises. One of the tree comparison's software tools, the Mesquite's Tree Set Viz module, allows the rapid and efficient visualization of the tree comparison distances usi...