Software Updates

EVcouplings

a tool to predict protein structure, function, and mutations using evolutionary sequence covariation.

MolScript

a program for creating schematic or detailed, publication-quality molecular graphics images from molecular 3D coordinates, usually, but not exclusively, protein structures.

IMOD

a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.

HKL2000

a data processing suite for X-ray crystallography that provides a sleek interface for devising a data collection strategy and processing data. HKL is based on the extended versions of Denzo, Xdisplayf and Scalepack. HKL was developed and is maintained by Wladek Minor (University of Virginia).

ShapeMapper2

a completely rewritten version of our ShapeMapper for reading out the results of an RNA chemical probing experiment by massively parallel sequencing that integrates careful handling of all classes of adduct-induced sequence changes, sequence variant correction, basecall quality filters, and quality-control warnings to identify RNA adduct sites.