Software Updates

deepTools

a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.

cryosparc-tools

a toolkit for interfacing with CryoSPARC.

bedtools

a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

CryoSieve

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

AWS CLI

(Amazon Web Services Command Line Interface) a command line interface tool to manage multiple Amazon Web Services and automate them through scripts.

cryoCARE

a restoration method that dramatically increases contrast in cryo-TEM images, improving the interpretability of the acquired data. PIP package memory efficient implementation of cryoCARE (Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data).

BCFtools

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.

breseq

a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads.

DeepChem

a high quality open-source toolchain that democratizes the use of deep-learning in drug discovery, materials science, quantum chemistry, and biology.

NGLView

a Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.

EternaFold

a tool that performs RNA secondary structure prediction.

doubleHelix

a tool for nucleic acid sequence identification, assignment and validation for cryo-EM and crystal structure models.

checkMySequence

a sequence assignment validation tool for in cryo-EM models

EMRNA

a deep learning based automated RNA modeling from cryo-EM maps.

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.

subTOM

(Subtomogram averaging scripts with TOM toolbox or Subvolume processing scripts with the TOM toolbox) a collection of scripts for a pipeline for subvolume alignment and averaging of electron cryo-tomography data.

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.

Dynamo2Relion

a tiny function to convert Dynamo tables to star files for RELION 4.0

LightDock

a protein-protein, protein-peptide and protein-DNA docking framework based on the Glowworm Swarm Optimization (GSO) algorithm.

Evo

a program for DNA foundation modeling from molecular to genome scale

Spring

(Single Particle Reconstruction from Images of kNown Geometry) a single-particle based helical reconstruction package for electron cryo-micrographs used to determine 3D structures of either highly ordered or less ordered specimens.

TomoNet

a software package with a modern graphical user interface to carry out the entire pipeline of cryoET and subtomogram averaging to achieve high resolution.

Ghostscript

an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be involved with gs command.

cs2star

a simple utility that wraps around csparc2star.py to convert particle positions from Cryosparc JOB directories into a RELION-ready directory.

Foldseek

a program that enables fast and sensitive comparisons of large structure sets.

Infernal

(INFERence of RNA ALignment) a program that searches DNA sequence databases for RNA structure and sequence similarities and uses a special case of profile stochastic context-free grammars called covariance models (CMs). In many cases It is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.