Mosaic is a software application to visually analyze sequence relationships. The similarities between the sequences of a given set are displayed within a matrix (mosaic plot), which enables the visual identification of clusters of related sequences, outliers or other sequences with special properties.
PSAAM (Protein Sequence Analysis And Modelling) includes many useful features for analysis of structural information from sequence data, cartoons for graphical representation of secondary structures, prediction programs, and prediction aids, a ribosome function for generation of coordinates sets in PDB format (including Header information) for viewing by molecular graphics packages (examples, see also PDVWIN), and a SeqPlot function for plotting secondary structural models (helical cylinders and wheels, coils, etc., with each residue indicated by a circle, color-coded (or coded by line thickness) according to the current physico-chemical index.
Mussa (Multi-Species Sequence Analysis) is a bioinformatics tool for finding and visualizing regions of conserved DNA by comparing across several species. It has been found that conserved regions are frequently enriched for regions that are functionally important. Thus Mussa is a tool to help discover previously unknown functional DNA elements.
AAScan (formely AlaScan) – batch primer design software for scanning mutagenesis
MutantChecker – helps to analyse the sequenceing results from scanning mutagenesis
PCR Cloning – design of primers for ligation-independent cloning
CloVR is a desktop application that integrates state-of-the-art genomic tools in a robust, user friendly, and fully automated software package with optional support for cloud computing platforms. CloVR currently bundles push-button pipelines for microbial genomics, including single-genome projects, 16S rRNA sequence analysis, and metagenomic sequencing projects. Additional pipelines for comparative genome analysis, prokaryotic and eukaryotic RNA-sequencing and viral genomics are planned.
GATA is a stand alone, platform independent, graphic alignment tool for comparative sequence analysis. It makese use of BLAST to graphically align two DNA sequences creating box-line-box representations of window scored local alignments. Gata can also display extensive gene annotation using a standardized GFF format.