In Galaxy TopHat has been replaced with HiSat or HiSat2. When following Galaxy tutorials replace TopHat commands with HiSat or HiSat2.
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
VolView is an intuitive, interactive system for volume visualization that allows researchers to quickly explore and analyze complex 3D medical or scientific data on a standard PC. Users can easily generate informative images and navigate the data for further analysis. 3D tools include composite and MIP volume rendering, contouring, cropping, and oblique reformatting. Segmentation can be performed, and resulting structures can be analyzed using distance, angle, surface area and volume measurement tools. Polygonal surface models can be exported for rapid prototyping.
The CRYSTAL program computes the electronic structure of periodic systems within Hartree Fock, density functional or various hybrid approximations. The Bloch functions of the periodic systems are expanded as linear combinations of atom centred Gaussian functions. Powerful screening techniques are used to exploit real space locality. The code may be used to perform consistent studies of the physical, electronic and magnetic structure of molecules, polymers, surfaces and crystalline solids.
HKL-2000 program package is based on the extended versions of Denzo, Xdisplayf and Scalepack. It consists of several subprograms coordinated by the graphical command center. The most important new elements are: strategy and simulation, 3-D processing, mosaicity refinement during processing, variable spot size, easy change of the space group, report generation, etc. The software is driven by the graphical user interface, which greatly improves convenience of working with various data sets.
The (Crystallographic Object)-Oriented Toolkit
Displays maps and models and allows certain model manipulations: idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, model validation and other stuff.
Coot is part of the CCP4 Molecular Graphics Project. The Molecular Graphics Project has a wide remit and crystallographic map fitting is a part of that. The Coot functions have their own interface and some of them will be integrated into CCP4mg in due course.
MacVector is a sequence analysis software for Macintosh computers. It provides sequence editing, primer design, Internet database searches, protein analysis, sequence confirmation, contig assembly capabilities, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a wide variety of other functions.
Notice to users:
Though still available for access MacVector will no longer be updated after 10/2014.
FingerPrinted Contigs (FPC) is an interactive program for building contigs from fingerprinted clones.