UNLABELLED: Phylogenetic trees with hundreds of thousands of leaves are now being inferred from sequence data, posing significant challenges for visualization and exploratory analysis. Image data supplying valuable context for species in trees (and cues for exploring them) are becoming increasingly available in biodiversity databases and elsewhere but have rarely been built into tree visualization software in a scalable way. Ceiba lets the user explore large trees and inspect image collection arrays (sets of 'homologous' images) comprising mixtures of 2D and 3D image objects. Ceiba exploits recent improvements in graphics hardware, OpenGL toolkits and many standard high-performance computer graphics strategies, such as texture compression, level of detail control, culling, animations and image caching. Its tree layouts can be tuned by user-provided phylogenetic definitions of subtrees. The code has been extensively tested on phylogenies of up to 55,000 leaves and images. AVAILABILITY AND IMPLEMENTATION: A manual, datasets, source code (distributed under GPL) and binaries for OS X are available at http://sourceforge.net/projects/ceiba. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The inositol trisphosphate receptor ([Formula: see text]) is one of the most important cellular components responsible for oscillations in the cytoplasmic calcium concentration. Over the past decade, two major questions about the [Formula: see text] have arisen. Firstly, how best should the [Formula: see text] be modeled? In other words, what fundamental properties of the [Formula: see text] allow it to perform its function, and what are their quantitative properties? Secondly, although calcium oscillations are caused by the stochastic opening and closing of small numbers of [Formula: see text], is it possible for a deterministic model to be a reliable predictor of calcium behavior? Here, we answer these two questions, using airway smooth muscle cells (ASMC) as a specific example. Firstly, we show that periodic calcium waves in ASMC, as well as the statistics of calcium puffs in other cell types, can be quantitatively reproduced by a two-state model of the [Formula: see text], and thus the behavior of the [Formula: see text] is essentially determined by its modal structure. The structure within each mode is irrelevant for function. Secondly, we show that, although calcium waves in ASMC are generated by a stochastic mechanism, [Formula: see text] stochasticity is not essential for a qualitative prediction of how oscillation frequency depends on model parameters, and thus deterministic [Formula: see text] models demonstrate the same level of predictive capability as do stochastic models. We conclude that, firstly, calcium dynamics can be accurately modeled using simplified [Formula: see text] models, and, secondly, to obtain qualitative predictions of how oscillation frequency depends on parameters it is sufficient to use a deterministic model.

UNLABELLED: Paloverde is a new program designed to help visualize the phylogenetic structure of moderately large trees--trees on the scale of 100-2500 leaf nodes. The program embeds the user in an interactive virtual 3D world in which a large tree presented in various layouts can be manipulated through a mouse interface. The program implements radial 2D layouts, and true 3D spiral, conical and hemispherical (i.e. truly 'tree'-like) layouts. Subclades can be defined in the input file (using standard node-based definitions) and displayed collapsed as new leaf nodes, or left intact but annotated with names around the periphery of the tree. A search tool lets the user zoom to any selected leaf node. Paloverde is an open source project written in ANSI C using the OpenGL library for 3D visualization. AVAILABILITY: Source code, makefiles for Mac OS X and Linux and a compiled binary for Mac OS X are available at http://ginger.ucdavis.edu/paloverde/paloverde.html, along with a sample dataset.

The input to a supertree problem is a collection of phylogenetic trees that intersect pairwise in their leaf sets; the goal is to construct a single tree that retains as much as possible of the information in the input. This task is complicated by inconsistencies due to errors. We consider the case where the input trees are rooted and are represented by the clusters they exhibit. The problem is to find the minimum number of flips needed to resolve all inconsistencies, where each flip moves a taxon into or out of a cluster. We prove that the minimum-flip problem is NP-complete, but show that it is fixed-parameter tractable and give approximation algorithms for special cases.

MOTIVATION: A noble and ultimate objective of phyloinformatic research is to assemble, synthesize, and explore the evolutionary history of life on earth. Data mining methods for performing these tasks are not yet well developed, but one avenue of research suggests that network connectivity dynamics will play an important role in future methods. Analysis of disordered networks, such as small-world networks, has applications as diverse as disease propagation, collaborative networks, and power grids. Here we apply similar analyses to networks of phylogenetic trees in order to understand how synthetic information can emerge from a database of phylogenies. RESULTS: Analyses of tree network connectivity in TreeBASE show that a collection of phylogenetic trees behaves as a small-world network-while on the one hand the trees are clustered, like a non-random lattice, on the other hand they have short characteristic path lengths, like a random graph. Tree connectivities follow a dual-scale power-law distribution (first power-law exponent approximately 1.87; second approximately 4.82). This unusual pattern is due, in part, to the presence of alternative tree topologies that enter the database with each published study. As expected, small collections of trees decrease connectivity as new trees are added, while large collections of trees increase connectivity. However, the inflection point is surprisingly low: after about 600 trees the network suddenly jumps to a higher level of coherence. More stringent definitions of 'neighbour' greatly delay the threshold whence a database achieves sufficient maturity for a coherent network to emerge. However, more stringent definitions of 'neighbour' would also likely show improved focus in data mining. AVAILABILITY: http://treebase.org

SUMMARY: Estimating divergence times and rates of substitution from sequence data is plagued by the problem of rate variation between lineages. R8s version 1.5 is a program which uses parametric, nonparametric and semiparametric methods to relax the assumption of constant rates of evolution to obtain better estimates of rates and times. Unlike most programs for rate inference or phylogenetics, r8s permits users to convert results to absolute rates and ages by constraining one or more node times to be fixed, minimum or maximum ages (using fossil or other evidence). Version 1.5 uses truncated Newton nonlinear optimization code with bound constraints, offering superior performance over previous versions. AVAILABILITY: The linux executable, C source code, sample data sets and user manual are available free at http://ginger.ucdavis.edu/r8s.