Treephyler: fast taxonomic profiling of metagenomes.

SUMMARY: Assessment of phylogenetic diversity is a key element to the analysis of microbial communities. Tools are needed to handle next-generation sequencing data and to cope with the computational complexity of large-scale studies. Here, we present Treephyler, a tool for fast taxonomic profiling of metagenomes. Treephyler was evaluated on real metagenome to assess its performance in comparison to previous approaches for taxonomic profiling. Results indicate that Treephyler is in terms of speed and accuracy prepared for next-generation sequencing techniques and large-scale analysis. AVAILABILITY: Treephyler is implemented in Perl; it is portable to all platforms and applicable to both nucleotide and protein input data. Treephyler is freely available for download at http://www.gobics.de/fabian/treephyler.php.

Periodic solutions and refractory periods in the soliton theory for nerves and the locust femoral nerve.

Close to melting transitions it is possible to propagate solitary electromechanical pulses which reflect many of the experimental features of the nerve pulse including mechanical dislocations and reversible heat production. Here we show that one also obtains the possibility of periodic pulse generation when the constraint for the nerve is the conservation of the overall length of the nerve. This condition generates an undershoot beneath the baseline ('hyperpolarization') and a 'refractory period', i.e., a minimum distance between pulses. In this paper, we outline the theory for periodic solutions to the wave equation and compare these results to action potentials from the femoral nerve of the locust (Locusta migratoria). In particular, we describe the frequently occurring minimum-distance doublet pulses seen in these neurons and compare them to the periodic pulse solutions.