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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 evolution:...
In practice, one is often faced with incomplete phylogenetic data, such as a collection of partial trees or partial splits. This paper poses the problem of inferring a phylogenetic super-network from such data and provides an efficient algorithm for doing so, called the Z-closure method. Application to a set of five published partial gene trees relating different fungal species illustrates the usefulness...
When multiple genes are used in a phylogenetic study, the result is often a collection of incompatible trees. Phylogenetic networks and super-networks can be employed to analyze and visualize the incompatible signals in such a data set. In many situations, it is important to have control over the amount of imcompatibility that is represented in a phylogenetic network, for example reducing noise by...
This paper continues our earlier investigations into the inversion of random functions in a general (abstract) setting. In Section 2, we investigate a concept of invertibility and the invertibility of the composition of random functions defined on finite sets. In Section 3, we resolve some questions concerning the number of samples required to ensure the accuracy of maximum likelihood estimation (MLE)...
The amalgamation of leaf-labeled trees into a single (super)tree that “displays” each of the input trees is an important problem in classification. We discuss various approaches to this problem and show that a simple and well-known polynomial-time algorithm can be used to solve this problem whenever the input set of trees contains a minimum size subset that uniquely determines the supertree. Our results...
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