Thomas Ludwig

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The ARB (from Latin arbor, tree) project was initiated almost 10 years ago. The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface. Although it was initially designed for ribosomal RNA data, it can be used for any nucleic and(More)
MOTIVATION The computation of large phylogenetic trees with statistical models such as maximum likelihood or bayesian inference is computationally extremely intensive. It has repeatedly been demonstrated that these models are able to recover the true tree or a tree which is topologically closer to the true tree more frequently than less elaborate methods(More)
Inference of phylogenetic trees comprising hundreds or even thousands of organisms based on the Maximum Likelihood (ML) method is computationally extremely intensive. In order to accelerate computations we implemented RAxML-OMP, an efficient OpenMP-parallelization for Symmetric Multi-Processing machines (SMPs) based on the sequential program RAxML-V(More)
Today's computational science demands have resulted in ever larger parallel computers, and storage systems have grown to match these demands. Parallel file systems used in this environment are increasingly specialized to extract the highest possible performance for large I/O operations, at the expense of other potential workloads. While some applications(More)
Summary form only given. Inference of phylogenetic trees comprising thousands of taxa using maximum likelihood is computationally extremely expensive. We present simple heuristics which yield accurate trees for simulated as well as real data and reduce execution time. The new heuristics have been implemented in a program called RAxML which is freely(More)
The computation of large phylogenetic trees with maximum likelihood is computationally intensive. In previous work we have introduced and implemented algorithmic optimizations in <b>PAxML.</b> The program shows run time improvements &gt; 25% over <b>parallel fastDNAml</b> yielding exactly the same results. This paper is focusing on computations of large(More)
Distributed computing infrastructures provided by sensor networks supports new ways of observing human motion. In this paper, we discuss algorithms that use data from sensor networks for tracking the gait of human walk. Three methods for identifying footsteps and footstep patterns that describe a walk of a subject are discussed. The methods interpret the(More)
RNA interference (RNAi) has emerged as a powerful technique for studying loss-of-function phenotypes by specific down-regulation of gene expression, allowing the investigation of virus-host interactions by large-scale high-throughput RNAi screens. Here we present a robust and sensitive small interfering RNA screening platform consisting of an experimental(More)