BioJS's vision is that 'every online biological dataset in the world should be visualized with BioJS tools'.
At this time, graphical displays of the TMAP alignment could only be visualized with separate tools for alignment and assembly viewing, such as the IGV package (Integrative Genomics Viewer [23]) which accepts BAM (binary alignment map), BAI (binary alignment index files) and other file formats.
In order to visualize the general landscape of gene expression in silico, gene expression in samples from autism were plotted versus the expression found in healthy controls to be visualized with the ViaComplex software, a tool that was previously developed and validated in our laboratory.
Although the presence of spillage, residue, penetration, and aspiration is visualized with either tool, there are many other findings that are important for the examiner to identify.
Nucmer alignments were visualized with the MUMmer tool Mummerplot.
Taken together, the whole-genome comparison maps were visualized with CGView Comparison Tool software as shown in Figure 3.
DNA sequence comparisons were visualized with the Artemis Comparison Tool (ACT [ 94]).
Detection of retroelements was performed with the MASiVE and LTRharvester tools (http://tools.bat.ina.certh.gr/masive/) (http://tools.bat.ina.certh.gr/ltrharvester/) and homology was visualized with Circoletto (http://tools.bat.ina.certh.gr/circoletto/), all three tools developed in-house at INA, by the Bioinformatics Analysis Team BATT).
Co-registered CT, SPECT, and SPECT/CT images were visualized with a commercially available 3D volume fusion tool (Syngo.via®, Siemens Healthcare).
Detection of retroelements was performed with the MASiVE and LTRharvester tools (http://tools.bat.ina.certh.gr/masive/) (http://tools.bat.ina.certh.gr/ltrharvester/) and homology was visualized with Circoletto (http://tools.bat.ina.certh.gr/circoletto/).bat.ina.certh.gr/circoletto/
