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Name Description Links
an Any-to-PostScript filter that processes plain text files, but also pretty prints quite a few popular languages.
Keywords:
Utilities
a program to format multiple sequence alignments in PostScript for publication and to assist in analysis. Alscript does not support point-and-click, but has a scripting language to allow complex effects.
Keywords:
Bioinformatics
allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures.
Keywords:
Nucleic Acids
a Python distribution that includes more than 400 of the most popular Python packages for science, math, engineering, and data analysis.
a program suite for small-angle scattering (SAXS) data analysis from biological macromolecules.

Restriction: available to nonprofit users who register with EMBL & submit confirmation to SBGrid.

Keywords:
SAXS
a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.
Keywords:
Utilities
a set of command line tools written in C and making use of the BiopLib library for manipulation of protein structure and sequence.
a set of tools for biological computation written in Python by an international team of developers.
Keywords:
Utilities
a program for analysis of SAXS data that enables creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced processing using GNOM, DAMMIF, and AMBIMETER. It also allows easy processing of inline SEC-SAXS data.
Keywords:
SAXS
(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.
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.
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.
a general purpose multiple sequence alignment program for DNA or proteins.
Keywords:
Bioinformatics
a multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.
Keywords:
Bioinformatics
redistributable software libraries to support CUDA applications for Linux.
Keywords:
Other
an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). It makes writing C extensions for Python as easy as Python itself. cython is installed as a module within python.
Keywords:
Other
Python Module
(ELECtron Tomography Resolution Assessment) a suite of programs written to estimate the resolution of electron density volumes obtained by electron tomography.
Keywords:
Tomography
integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
(Easy Sequencing in Postscript) a utility to generate a pretty PostScript output from aligned sequences and coordinate files.
Keywords:
Bioinformatics
a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.
an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.
Keywords:
Utilities
a popular way to view DNA sequence traces on Linux, Mac OSX, Windows, and Solaris. FinchTV started as the only chromatogram viewer that can display an entire trace in a scalable multi-pane view. And it leads the way with raw data views, BLAST searching and the ability to reverse complement sequences and traces.
Keywords:
Bioinformatics
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.
a powerful and comprehensive suite of molecular biology tools.

Restriction: 13-seat floating license available to non-profit groups.

Keywords:
Bioinformatics
an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be involved with gs command.
Keywords:
Other
Utilities
creates a Globus endpoint on your laptop or other personal computer and allows you to transfer and share files, regardless of whether you have administrative privileges on your machine. Globus Connect Personal is available for Mac OS X and Linux operating systems.
Keywords:
Other
Utilities
a portable command-line driven graphing utility originally created to allow scientists and students to visualize mathematical functions and data interactively. It has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like CCP4.
Keywords:
Utilities
a general plotting, curve fitting and data transformation program.
Keywords:
Utilities
an open-source graph visualization software program. A gallery of images is available on the developer's website: http://www.graphviz.org/Gallery.php
Keywords:
Utilities
a modular program for SPM (scanning probe microscopy) data visualization and analysis.
a high quality visualizer and annotator for three dimensional molecular structures, sequences, alignments, chemical spreadsheets and biological data.
a simple, user-friendly tool for image classification and segmentation in up to three spatial and one spectral dimension. Using it requires no experience in image processing.
Keywords:
Utilities
a software suite to create, edit, compose, or convert bitmap images.
Keywords:
Utilities
(Image Processing Library & Toolbox) a 2D Crystallography Suite developed by Andreas Schenk.
Keywords:
2DX
provides a architecture for interactive computing with a browser-based notebook where you can combine code, text, mathematical expressions, inline plots, and other rich media into a single document and support for interactive data visualization. IPython is now part of the larger Jupyter project. Please see the [Jupyter website](http://jupyter.org/index.html) for more information. IPython is installed as a module within python ...
Keywords:
Python Module
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. To use Jalview on OS X, you will need to install Java: *
Keywords:
Bioinformatics
a system designed for automated collection of images from a transmission electron microscope; it includes the python-side programs written in python and c, the MySQL database and server, and the mainly php-based image and data viewers on a web server.
Keywords:
Bioimaging
a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).
(Minimal Ensemble Search) a genetic algorithm used to identify the minimal ensemble required to best fit experimental data. The simulations provide an ensemble of molecular models from which a SAXS curve is calculated and compared to the experimental curve. Written by Martin Pelikan and Michal Hammel at Lawrence Berkeley Laboratory.
Keywords:
SAXS
a series of software tools for docking flexible ligands into receptors with selective flexibility: AutoDockFR: a docking engine using the AutoDock4 forcefield; AutoGridFR: a graphical user interface for setting up docking boxes; AutoSite: a ligand binding site detection and characterization program.
(Mixture of Isoforms model) for isoform quantitation using RNA-Seqis 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.
(MOLecular PHYlogenetics) a computer program package for molecular phylogenetics.
Keywords:
Bioinformatics
an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.
Keywords:
Other
a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
(multiple sequence comparison by log-expectation) a public domain multiple alignment software for protein and nucleotide sequences.
Keywords:
Bioinformatics
a multi-purpose text editor for the X Window System, which combines a standard, easy to use, graphical user interface with thorough functionality and stability.
Keywords:
Utilities
a simple command-line program that allows you to submit a single file of FASTA sequences over an internet connection to the NCBI BLAST databases. Searches are submitted through the client to the NCBI servers and do not need to download the databases locally (also called netblast and blastcl3).
Keywords:
Bioinformatics
contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. NumPy is installed as a module within Python.
Keywords:
Other
Python Module
a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
Keywords:
Utilities
(Open Java Development Kit) is a free and open source implementation of the Java Platform, Standard Edition (Java SE).
Keywords:
Other
a library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language. pandas is installed as a module within python.
(Particle Estimation for Electron Tomography) a package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.
Keywords:
Tomography
(Pathologically Eclectic Rubbish Lister or sometimes called the Practical Extraction and Reporting Language) a highly capable, feature-rich family of programming languages.
Keywords:
Other
Utilities
a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs.
Keywords:
Utilities
a free package of software programs for inferring phylogenies.
(Protein-Ligand Interaction Profiler) for automated detection and visualization of relevant non-covalent protein-ligand contacts in 3D structures. Available as a stand alone application or a web service.
a multipurpose X11 plotting program that specializes in contour plots but can also handle 2D and 3D plots. The plot-types supported are: contour plots (rectangular grid, as well as triangular mesh), 2D line and scatter plots (x-vs-y), 3D surface , line and scatter plots, vector plots, probability plots, histograms, barcharts. The program has an rough but functional Graphical User Interface, through which it is possible ...
Keywords:
Utilities
a GNU package containing software for programmers and technical users. Its centerpiece is libplot, a powerful C/C++ function library for exporting 2-D vector graphics in many file formats, both vector and raster. It can also do vector graphics animations. libplot is device-independent in the sense that its API (application programming interface) does not depend on the type of graphics file to be exported ...
Keywords:
Utilities
a newly designed NMR chemical shift guided protein structure alignment method to generate protein templates with the best matched local structure from the Protein Data Bank.
(Persistence of Vision Raytracer) a high-quality, totally free tool for creating stunning three-dimensional graphics. It is available in official versions for Windows, Mac OS/Mac OS X and i86 Linux. The source code is available for those wanting to do their own ports. POVRAY was originally written by David Kirk Buck and Aaron A. Collins.
Keywords:
Utilities
a widely used program that designs PCR primers (PCR = "Polymerase Chain Reaction"). Primer3 can also design hybridization probes and sequencing primers.
Keywords:
Bioinformatics
an efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.
Keywords:
Bioinformatics
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.
Keywords:
Tomography
a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability. Its syntax allows programmers to express concepts in fewer lines of code than would be possible in languages such as C++ or Java, thus overall, allowing programmers to work more quickly and integrate their systems more effectively. Python includes the following scientific modules: Appion, Cython, iPython Notebook, Miso, NumPy, Pandas, ProDy ...
Keywords:
Other
Utilities
unifies standard tomogram processing steps in a single python-based toolbox. For subtomogram averaging, we implemented an adaptive adjustment of scoring and sampling that clearly improves the resolution of averages compared to static strategies.
cross platform time zone library that brings the Olson tz database into Python and allows accurate and cross platform timezone calculations using Python 2.4 or higher. It also solves the issue of ambiguous times at the end of daylight saving time, which you can read more about in the Python Library Reference (datetime.tzinfo).
Keywords:
Bioimaging
Other
a cross-platform application framework that is used for developing application software that can be run on various software and hardware platforms with little or no change in the underlying codebase, while still being a native application with native capabilities and speed.
Keywords:
Other
a free software environment for statistical computing and graphics.
Keywords:
Other
Utilities
a fast, versatile and program for docking ligands to proteins and nucleic acids.
Keywords:
Bioinformatics
a program for measuring the resolution of single-particle reconstructions.
a modular toolkit developed to deal with RNA structure probing and post-transcriptional modifications mapping high-throughput data. Toolkit will help with automatic reference transcriptome creation, automatic reads preprocessing (adapter clipping and trimming) and mapping, scoring and data normalization, and accurate RNA folding prediction by incorporating structural probing data.
a complete package for RNA and DNA secondary structure prediction and analysis.
an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
Keywords:
Other
a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.
Keywords:
Utilities
a program suite used to create atomistic models of molecular systems and to compare scattering data from these models directly to experimental data.
Keywords:
SAXS
the program suite SASSIE (tools used to create atomistic models of molecular systems and to compare scattering data from these models directly to experimental data) plus “courtesy modules,” which include the molecular dynamics package NAMD, the scattering calculators Cryson and Crysol, and the program Hydropro for calculating hydrodynamic properties.

Restriction: available to nonprofit users who register with EMBL and send confirmation to SBGrid.

Keywords:
SAXS
a plotting facility for SAXS-data, as well as a convenient tool to quickly generate plots for publication. Saxsview shows 1D-data in .dat, .int, .fit and .fir formats of the ATSAS package, the cansas .xml format (v1.0), as well as .csv files.
Keywords:
SAXS
a graphical installation client used to install the SBGrid software collection on Apple OSX computers running MacOSX v10.9 - 10.12. Users can cherrypick a subset of applications for installation on their laptops or desktops. Software updates are highlighted, but users trigger the software update manually at their convenience.
a JAVA-based application for basic analysis of SAXS datasets. Scatter is developed by Robert Rambo at the Diamond Light Source (Didcot, UK). The program was previously developed at the SIBYLS beamline (12.3.1) of the Advanced Light Source, Berkeley, CA.
Keywords:
SAXS
a suite of programs for sequence alignment including: aln, swg, prrn, phyln and makmdm. aln: Pairwise alignment of biological sequences supporting spliced alignment procedures. swg: locally aligns a pair of DNA or protein sequences by Smith-Waterman-Gotoh algorithm. Currently spliced alignment is not supported. Profile version is very slow. prrn: global multiple alignment of a set of protein or DNA sequences by doubly nested iterative ...
Keywords:
Bioinformatics
(pronounced “Sigh Pie”) a Python-based ecosystem of open-source software for mathematics, science, and engineering. In particular, these are some of the core packages: NumPy, SciPy Library, Matplotlib, IPython, Sympy, pandas
Keywords:
Python Module
an interactive multi-resolution docking and visualization program for low-resolution density maps and atomic structures.
converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots, and provides extensive diagnostic information useful for experiment analysis and troubleshooting.
(Sequence Search and Alignment by Hashing Algorithm) a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences. SSAHA2 reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package.
Keywords:
Bioinformatics
a set of DNA sequence assembly, editing and analyzing tools. Developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
Keywords:
Bioinformatics
a program to recognize secondary structural elements in proteins from their atomic coordinates.
a pipeline that uses data obtained from ShapeMapper to model RNA secondary structures, including pseudoknots; identify de novo regions with well-defined and stable structures; and visualize most probable and alternative helices.
(Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches.
a multiple sequence alignment package that can be used to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment (M-Coffee).
Keywords:
Bioinformatics
cleans up raw data files and converts them to pdf format with LaTex. TeX Live offers an easy way to get up and running with the TeX document production system.
Keywords:
Utilities
a Python-based program package that can be used to efficiently detect and characterize significant conformational changes in simulated biomolecular systems.
a graphical front end to the diff program. It provides a side-by-side view of the differences between two files, along with several innovative features such as diff bookmarks and a graphical map of differences for quick navigation.
Keywords:
Utilities
a software package for comprehensive analysis of hydrodynamic data from analytical ultracentrifugation experiments.
Keywords:
Utilities
a comprehensive data analysis software package for hydrodynamic data from analytical ultracentrifugation experiments. It is the latest multi-platform version of UltraScan, which replaced the UltraScan II distribution. UltraScan II development has stopped although it is still available.
Keywords:
Utilities
performs automated NMR data analysis for protein 3D structure determination. UNIO represents the result of more than a decade of innovative research performed in order to enable accurate, objective and highly automated protein structure determination by NMR.
Keywords:
Nucleic Acids
(Visualization Tool Kit)f a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including scalar, vector, tensor, texture, and volumetric methods, as well as advanced modeling techniques such as implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.
wxPython: a blending of the wxWidgets C++ class library with the Python programming language.
a two-dimensional molecule drawing program for Unix operating systems that can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS.
Keywords:
Utilities
an interactive image manipulation program for the X Window System. It can operate on images in the GIF, JPEG, TIFF, PBM, PGM, PPM, XPM, X11 bitmap, Sun Rasterfile, Targa, RLE, RGB, BMP, PCX, FITS, and PM formats on all known types of X displays. It can generate PostScript files, and if you have ghostscript (version 2.6 or above) installed on your machine, it ...
Keywords:
Utilities
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