BEAST: Bayesian evolutionary analysis by sampling trees

<p>Abstract</p> <p>Background</p> <p>The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented.</p> <p>Results</p> <p>BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at <url>http://beast-mcmc.googlecode.com/</url> under the GNU LGPL license.</p> <p>Conclusion</p> <p>BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.</p

Density functionals, with an option-pricing application

We present a method of estimating density-related functionals, without prior knowledge of the density’s functional form. The approach revolves around the specification of an explicit formula for a new class of distributions that encompasses many of the known cases in statistics, including the normal, gamma, inverse gamma, and mixtures thereof. The functionals are based on a couple of hypergeometric functions. Their parameters can be estimated, and the estimates then reveal both the functional form of the density and the parameters that determine centering, scaling, etc. The function to be estimated always leads to a valid density, by design, namely, one that is nonnegative everywhere and integrates to 1. Unlike fully nonparametric methods, our approach can be applied to small datasets. To illustrate our methodology, we apply it to finding risk-neutral densities associated with different types of financial options. We show how our approach fits the data uniformly very well. We also find that our estimated densities’ functional forms vary over the dataset, so that existing parametric methods will not do uniformly well