Software Updates

PyEM

Python modules and command-line utilities for electron microscopy of biological samples.

Scipion

an image processing framework to obtain 3D models of macromolecular complexes using 3D EM that allows you to execute workflows combining different software tools, while taking care of formats and conversions.

Emap2sec+

a computational tool using deep learning that can accurately identify structures, alpha helices, beta sheets, other(coils/turns) and DNA/RNA, in cryo-EM maps of medium to low resolution.

seaview

is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.

R-pkgs-SBGrid

contains optional R pkgs

Jalview

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.

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.

IceBreaker

software for ice gradient estimation and removal on cryoEM micrographs.

PyRosetta

an interactive Python-based interface to the powerful Rosetta molecular modeling suite that enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.

Schrodinger

a suite of tools for drug discovery. The Schrodinger suite runs on Linux and Mac workstations, but due to its size, it is not included in our default installation.