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.
ITSx is a tool similar but more advanced to V-Xtractor and has been designed to extract internal transcribed spacer (ITS) regions from eukaroytic ribosomal operons. It also uses Hidden Markov Models to locate the coding regions (i.e. SSU, 5.8S, LSU) adjacent to ITS1 and ITS2. ITSx has been developed by Johan Bengtsson-Palme and R. Henrik Nilsson at the University of Gothenburg. ITSx replaces the FungalITSextractor tool previously developed by R. Henrik Nilsson.
V-RevComp is a Perl-based, high-throughput software tools that uses hidden Markov models to detect the conserved loci of rRNA genes in order to determine its orientation. Reverse complementary DNA sequences - sequences that are inadvertently given backwards with all purines and pyrimidines transposed - can affect sequence analysis detrimentally unless taken into account. 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 (see publication for further details).
ITS-RevComp, a reverse complementary orientation checker also exists for internal transcribed spacer regions. It also uses Hidden Markov Models to locate the coding regions (i.e. SSU, 5.8S, LSU) adjacent to ITS1 and ITS2 and subsequently detects and reorients reverse complementary sequences. The tools has been developed by R. Henrik Nilsson at the University of Gothenburg.
Metaxa2 is an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets (e.g. shotgun metagenomes) and assign them to an archaeal, bacterial, nuclear eukaryote, mitochondrial, or chloroplast origin. Using data from reference databases and from full-length organelle and organism genomes, Metaxa detects and scores SSU sequences for origin with very low proportions of false positives and negatives. Metaxa is under constant development by Johan Bengtsson-Palme and R. Henrik Nilsson at the University of Gothenburg.
Megraft is a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in metagenomes. Megraft has been developed by Johan Bengtsson-Palme and R. Henrik Nilsson at the University of Gothenburg.
Crunchclust is an efficient clustering algorithm that is capable of handling the most common Roche's 454 sequencing error (homopolymers). It uses Levenshtein distance for sequence comparison during clustering. It is also used successfully for the clustering of Illumina Miseq sequences. The software has been developed by Dipankar Bachar and Richard Christen.