RNAmmer: Rapid annotation of ribosomal RNA genes

RNAmmer is a widely used tool for identifying ribosomal RNA genes in genome sequences. It uses hidden Markov models to predict major rRNA species across all kingdoms of life and was designed to improve consistency in genome annotation. 

Genome Atlas / CBS Genome Atlas: Visualizing whole-genome structure at a glance

The Genome Atlas framework provides graphical summaries of microbial chromosomes, including genome composition, AT content, gene features, tRNA/rRNA counts, base skews, repeats, curvature, and other DNA structural features. This work helped establish genome-scale visualization as a practical approach for comparing bacterial genomes.

CMG-Biotools: A comparative microbial genomics workbench

CMG-Biotools is a free comparative genomics environment designed for users with limited computational experience. It supports analyses such as 16S rRNA phylogeny, DNA and codon statistics, proteome comparisons using BLAST, and graphical analysis of DNA structure.