BACKGROUND: Accurate taxonomy is best maintained if species are arranged as hierarchical groups in phylogenetic trees. This is especially important as trees grow larger as a consequence of a rapidly expanding sequence database. Hierarchical group names are typically manually assigned in trees, an approach that becomes unfeasible for very large topologies. RESULTS: We have developed an automated iterative procedure for delineating stable (monophyletic) hierarchical groups to large (or small) trees and naming those groups according to a set of sequentially applied rules. In addition, we have created an associated ungrouping tool for removing existing groups that do not meet user-defined criteria (such as monophyly). The procedure is implemented in a program called GRUNT (GRouping, Ungrouping, Naming Tool) and has been applied to the current release of the Greengenes (Hugenholtz) 16S rRNA gene taxonomy comprising more than 130,000 taxa. CONCLUSION: GRUNT will facilitate researchers requiring comprehensive hierarchical grouping of large tree topologies in, for example, database curation, microarray design and pangenome assignments. The application is available at the greengenes website 1.

BACKGROUND: In many contexts, researchers need specific primers for all sequences in a family such that each primer set amplifies only its target sequence and none of the others, e.g. to detect which transcription factor out of a family of very similar proteins that is present in a sample, or to design diagnostic assays for the identification of pathogen strains. RESULTS: This paper presents primique, a new graphical, user-friendly, fast, web-based tool which solves the problem: It designs specific primers for each sequence in an uploaded set. Further, a secondary set of sequences not to be amplified by any primer pair may be uploaded. Primers with high sequence similarity to non-target sequences are selected against. Lastly, the suggested primers may be checked against the National Center for Biotechnology Information databases for possible mis-priming. CONCLUSION: Results are presented in interactive tables, and various primer properties are listed and displayed graphically. Any close match alignments can be displayed. Given 30 sequences, the running time of primique is about 20 seconds.primique can be reached via this web address: http://cgi-www.daimi.au.dk/cgi-chili/primique/front.py.

BACKGROUND: The need to depict a phylogeny, or some other kind of abstract tree, is very frequently experienced by researchers from a broad range of biological and computational disciplines. Thousands of papers and talks include phylogeny figures, and often during everyday work, one would like to quickly get a graphical display of, e.g., the phylogenetic relationship between a set of sequences as calculated by an alignment program such as ClustalW or the phylogenetic package Phylip. A wealth of software tools capable of tree drawing exists; most are comprehensive packages that also perform various types of analysis, and hence they are available only for download and installing. Some online tools exist, too. RESULTS: This paper presents an online tool, PHY.FI, which encompasses all the qualities of existing online programs and adds functionality to hopefully eliminate the need for post-processing the phylogeny figure in some other general-purpose graphics program. PHY.FI is versatile, easy-to-use and fast, and supports comprehensive graphical control, several download image formats, and the possibility of dynamically collapsing groups of nodes into named subtrees (e.g. "Primates"). The user can create a color figure from any phylogeny, or other kind of tree, represented in the widely used parenthesized Newick format. CONCLUSION: PHY.FI is fast and easy to use, yet still offers full color control, tree manipulation, and several image formats. It does not require any downloading and installing, and thus any internet user regardless of computer skills, and computer platform, can benefit from it. PHY.FI is free for all and is available from this web address: http://cgi-www.daimi.au.dk/cgi-chili/phyfi/go.

We present a graphical user interface (GUI) for easy, intuitive control of a group of mobile robots moving in formation, and we give a short description of the general, local, distributed formation algorithm underlying the GUI. In spite of the high level of abstraction of the GUI, it captures the full functionality of the algorithm. The GUI has been tested with robots running in a simulator, and the formation algorithm itself has also been tested with real robots. We show results from experiments in both scenarios.

We study the problem of achieving global behavior in a group of distributed robots using only local sensing and minimal communication, in the context of formations. The goal is to have N mobile robots establish and maintain some predetermined geometric shape. We report results from extensive simulation experiments, and 40+ experiments with four physical robots, showing the viability of our approach. The key idea is that each robot keeps a single friend at a desired angle /spl theta/, using some appropriate sensor. By panning the sensor by /spl theta/ degrees, the goal for all formations becomes simply to center the friend in the sensor's field of view. We also present a general analytical measure for evaluating formations and apply it to the position data from both simulation and physical robot experiments. We used two lasers to track the physical robots to obtain ground truth validation data.

We report work on a LEGO robot that displays different emotional expressions in response to physical stimulation, for the purpose of social interaction with humans. This is a first step toward our longer-term goal of exploring believable emotional exchanges to achieve plausible interaction with a simple robot. Drawing inspiration from theories of human basic emotions, we implemented several prototypical expressions in the robot's caricatured face and conducted experiments to assess the recognizability of these expressions.