This study describes an automated framework for lineage designation from phylogenetic and genomic data, designed to scale to very large viral datasets while remaining consistent and interpretable.
This paper shows how SHAPE-guided RNA folding is implemented in the ViennaRNA Package, comparing three widely used strategies for turning nucleotide reactivities into soft constraints that improve thermodynamic structure prediction.
ViennaNGS is a modular toolbox for building reproducible NGS analysis workflows, combining Perl library code, utility scripts, and browser-oriented data-export components for early high-throughput genomics pipelines.
This paper revisits the earlier flooding-based landscape methods and adapts them to RNA secondary structures with a local, memory-efficient enumeration strategy.
TSSAR introduced statistically grounded, automated annotation of bacterial transcription start sites from dRNA-seq data and packaged it as both a RESTful web service and a standalone tool.