SBGridTV
a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
(Computer Aided Resonance Assignment) an application for the analysis of NMR spectra and computer-aided resonance assignment.
a versatile, integrated software system for the analysis, rebuilding, and visualization of 3-dimensional nucleic acid structures.
(Dissecting the Spatial Structure of RNA) a software tool for dissecting the spatial structure of RNA.
(Multi-Conformation Continuum Electrostatics) a biophysics simulation program combining continuum electrostatics and molecular mechanics. In this program, the protein side chain motions are simulated explicitly while the dielectric effect of solvent and bulk protein material is modeled by continuum electrostatics.
a tool that helps redistributable software libraries to support CUDA applications for Linux.
a multiple sequence alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) but is available as a general purpose alignment editor.
a merged hkl-file into k subsets with the number of reflections marked with -1; crossflaghkl partitions.
an open source library for free energy calculations in molecular systems that works with some of the most popular molecular dynamics engines. Perform free energy calculations as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation-based steered MD.
