V-RevComp is written in Perl and uses hidden Markov models to detect the conserved loci of rRNA genes in order to determine its orientation. The software supports sequence lengths ranging from full-length down to the short reads that are characteristic of next generation sequencing technologies. This tool is highly efficient in detecting and reorienting reverse complementary ribosomal sequences of almost any length and can additionally be used to detect various sequence anomalies.
V-Xtractor is a Perl-based, high-throughput software tool that locates, verifies, and extracts defined segments of sequence information from sequence datasets. Hidden Markov Models are used to detect the conserved boundaries of the target region and to extract the interjacent sequence information (that is for example the hyper-variable regions of the rRNA gene or the internal transcribed spacer regions of the rRNA operon). This tool extracts phylogenetically comparable regions without prior multiple sequence alignments and improves reliability of the data by confirming basic authenticity of the sequence.
Metaxa2 is a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets