Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods

Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods

The reconstruction of phylogenies is becoming an increasingly simple activity. This is mainly due to two reasons: the democratization of computing power and the increased availability of sophisticated yet user-friendly software. This review describes some of the latest additions to the phylogenetic toolbox, along with some of their theoretical and practical limitations. It is shown that Bayesia...

Expanding the UniFrac Toolbox

The UniFrac distance metric is often used to separate groups in microbiome analysis, but requires a constant sequencing depth to work properly. Here we demonstrate that unweighted UniFrac is highly sensitive to rarefaction instance and to sequencing depth in uniform data sets with no clear structure or separation between groups. We show that this arises because of subcompositional effects. We i...

Bayesian phylogenetic inference via Markov chain Monte Carlo methods.

We derive a Markov chain to sample from the posterior distribution for a phylogenetic tree given sequence information from the corresponding set of organisms, a stochastic model for these data, and a prior distribution on the space of trees. A transformation of the tree into a canonical cophenetic matrix form suggests a simple and effective proposal distribution for selecting candidate trees cl...

Expanding the Toolbox: Methods to Study and Refine Patient-Centered Medical Home Models

Towards a Toolbox for Geographic User Interfaces

User interfaces are a prominent part of applications that manipulate graphic data (geography, car-tography, CAD/CAM, ...). Although some work has been done recently in this area, each system usually has its own ad hoc user interface built from scratch, and there is no user interface model general enough for customizing the presentation of a speciic application which handles graphic data. This p...