Software Updates

R

a free software environment for statistical computing and graphics.

Clustal Omega

a multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.

HHsuite

an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

OpenMPI

an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.

RELION

(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

ImageJ

a Java image processing program inspired by NIH Image that can display, edit, analyze, process, save and print 8-bit, 16-bit, and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw" and supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations can be performed in parallel with other operations.

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.

MISO

a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples.

MISO is installed as a standalone program and as a module within python.

EVcouplings

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