Software Updates

IMP

(Integrative Modeling Platform) a program designed to allow mixing and matching of existing modeling components as well as the easy addition of new functionality.

EMReady

a tool that improves the quality and interpretability of cryo-EM maps by local and non-local deep learning

SAMtools

(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.

Chimera

a highly extensible, interactive molecular graphics program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. It is often a tool of choice for rendering EM volumes.

GROMACS

a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.

Dynamo-tools

a collection of tools for subtomogram averaging in dynamo.

Bowtie 2

an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

NAMD

a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Protomo

a system that includes programs and shell scripts for electron tomography of thin specimens, providing an interactive graphical tool for fast initial alignment of a tilt series, shell scripts for the more time consuming refinement, and some other useful image manipulation utilities.

CryoSieve

an advanced software solution designed for particle sorting/sieving in single particle analysis (SPA) for Cryogenic Electron Microscopy (cryo-EM).

PHENIX

(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.

MotionCor3

a multi-GPU program that corrects beam-induced sample motion on dose fractionated movie stacks. It implements a robust iterative alignment algorithm that delivers precise measurement and correction of both global and non-uniform local motions at single pixel level across the whole frame, suitable for both single-particle and tomographic images.

AreTomo2

(Alignment and Reconstruction for Electron Tomography 2) is a GPU-accelerated software package that provides an integrated solution to both fiducial-free alignment and reconstruction for cryoEM tomography.

aria2

a lightweight multi-protocol & multi-source command-line download utility. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink. aria2 can be manipulated via built-in JSON-RPC and XML-RPC interfaces.

TomoAND

a package for noise reduction in electron tomography with Anisotropic Nonlinear Diffusion.

IGV

(Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

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).

Focus

an interface for cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner, while new data is being acquired at the microscope.

XDS

(X-ray Detector Software) a software tool for processing single-crystal monochromatic diffraction data recorded by the rotation method.

TomoTwin-cryoet

a deep metric learning based particle picking procedure for cryo-ET

DIALS

(Diffraction Integration for Advanced Light Sources) a software project for the analysis of crystallographic diffraction images for many new methods from shutterless, fine-sliced rotation scans to randomly-oriented snapshots of serial crystallography. It uses multiple CPU and GPU machines to increase speed and accuracy based on a comprehensive physical model.

Chroma

a generative model for designing proteins programmatically.

ChimeraX

a tool of the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.

BLAST+

a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.