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Name Description Links
an interactive perl/tk application that can read common sequence alignment formats that the user can then alter, embellish, markup, etc. to produce the kind of sequence figure commonly found in biochemical articles.
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.
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a tool that allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures.
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.
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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
Other
(Amazon Web Services Command Line Interface) a command line interface tool to manage multiple Amazon Web Services and automate them through scripts.
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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 …
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a set of command line tools written in C and making use of the BiopLib library for manipulation of protein structure and sequence.
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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.
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SAXS
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(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 3D creation suite that supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking.
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 software for protein residue-residue Contacts from Correlated Mutations PREDicted quickly and accurately.
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a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
a general purpose multiple sequence alignment program for DNA or proteins.
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a multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.
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a tool that makes Run VS Code on any machine anywhere and access it in the browser.
a tool that enables the easy detection of CRISPRs and cas genes in user-submitted sequence data (allows sequences up to 50 Mo otherwise download standalone program). This is an update of the CRISPRFinder program with improved specificity and indication on the CRISPR orientation. MacSyFinder is used to identify cas genes, the CRISPR-Cas type and subtype.
a tool that helps redistributable software libraries to support CUDA applications for Linux.
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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.
(DENsity from Solution Scattering) an algorithm used for calculating ab initio electron density maps directly from solution scattering data.
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SAXS
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(ELECtron Tomography Resolution Assessment) a suite of programs written to estimate the resolution of electron density volumes obtained by electron tomography.
a program that 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.
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a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.
an application for Efficient Data Transfers which is capable of reading and writing at disk speed over wide area networks (with standard TCP). It is written in Java, runs an all major platforms and it is easy to use.
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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.
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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.
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a set of tools and libraries for interacting with Google Cloud products and services.
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a powerful and comprehensive suite of molecular biology and NGS analysis tools.

Restriction: shared license available to non-profit groups as add-on option.
an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be involved with gs command.
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(Globus Command Line Interface) a command line wrapper over the Globus SDK for Python. It is a standalone application that can be installed on the user’s machine and used to access the Globus service.
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a versatile markdown tool offering both a text-based user interface (TUI) for interactive browsing and a command-line interface (CLI) for direct manipulation of markdown content.
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a tool that superimposes molecular subunits into the density map of their complex. To reduce computational costs for the superimposing, both subunits and complexes are transformed into GMM (Gaussian Mixture Model) using the gmconvert program. Although designed to superimpose multiple atomic models of subunits into a low-resolution 3D density map, gmfit can also be applied to superimposing two 3D density maps or two atomic …
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 and Octave.
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a general plotting, curve fitting and data transformation program.
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an open-source graph visualization software program. A gallery of images is available on the developer's website: http://www.graphviz.org/Gallery.php
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a modular program for SPM (scanning probe microscopy) data visualization and analysis.
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(Hypergeometric Optimization of Motif EnRichment) a suite of sequencing analysis and sequence motif discovery tools.
a simple, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection.
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a software suite to create, edit, compose, or convert bitmap images.
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(Image Processing Library & Toolbox) a 2D Crystallography Suite developed by Andreas Schenk.
a lightweight and flexible command-line JSON processor.
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a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.
a language-agnostic HTML notebook application for Project Jupyter.
a program for the next-generation web-based user interface for Project Jupyter. JupyterLab enables you to work with documents and activities such as Jupyter notebooks, text editors, terminals, and custom components in a flexible, integrated, and extensible manner.
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.
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SAXS
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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.
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a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
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(multiple sequence comparison by log-expectation) a public domain multiple alignment software for protein and nucleotide sequences.
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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.
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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).
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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.
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(Open Java Development Kit) a free and open source implementation of the Java Platform, Standard Edition (Java SE).
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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.
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.
a swiss army knife for manipulating and editing PDB files.
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a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs.
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a free package of software programs for inferring phylogenies.
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(Protein-Ligand Interaction Profiler) a tool 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.
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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. plotutils also contains command-line programs for plotting scientific data, many of which use libplot to export graphics.
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(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.
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a widely used program that designs PCR primers (PCR = "Polymerase Chain Reaction"). Primer3 can also design hybridization probes and sequencing primers.
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an efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.
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a general purpose program for protein design, to redesign entire proteins or functional sites such as ligand-binding pockets. It uses a physics-based energy function and a stochastic method to search sequence and conformation space and allows users to directly select mutations that increase ligand binding free energy or ligand specificity. It can perform constant-pH Monte Carlo, which yields acid/base constants or pKa’s.
a python package for processing x-ray scattering data, first developed at the X9 beamline at NSLS, but revised multiple times and now in use at the LiX beamline at NSLS-II.
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SAXS
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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 in C++ or Java, thus allowing programmers to work more quickly and integrate their systems more effectively.
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a free software environment for statistical computing and graphics.
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a fast, versatile and program for docking ligands to proteins and nucleic acids.
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a program for measuring the resolution of single-particle reconstructions.
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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.
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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.
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a program suite used to create atomistic models of molecular systems and to compare scattering data from these models directly to experimental data.
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SAXS
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a set of 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
Other
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.
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SAXS
Other
an application for managing an SBGrid software installation. Users can choose a subset of applications for installation on their laptops or desktops or configure site installations for clusters, servers or cloud resources. This version is the command-line interface. A graphical version is available for download on the SBGrid wiki : [https://sbgrid.org/wiki/client_downloads](https://sbgrid.org/wiki/client_downloads) .
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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
Other
a suite of programs for sequence alignment: 1) aln: Pairwise alignment of biological sequences supporting spliced alignment procedures; 2) swg: locally aligns a pair of DNA or protein sequences by Smith-Waterman-Gotoh algorithm; 3) prrn: global multiple alignment of a set of protein or DNA sequences by doubly-nested iterative refinement method; 4) phyln: UPGMA or NJ method to make a phylogenetic tree from a multiple …
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a tool that converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots, and provides extensive diagnostic information useful for experiment analysis and troubleshooting.
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an R package that provides functions for inferring continuous, branching lineage structures in low-dimensional data. Designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering, Slingshot is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.
(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.
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a set of DNA sequence assembly, editing and analyzing tools developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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(STructural Alignment of Multiple Proteins) a suite of programs to compare and align protein 3-D structures. It will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position. It will also search a database of protein structures to identify structurally similar proteins and includes a number of utility programs for the manipulation of protein structures.
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).
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a system that cleans up raw data files and converts them to pdf format with LaTex. Offers an easy way to get up and running with the TeX document production system.
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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.
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a tool for the conversion of microED data collected on TVIPS TemCam-F416, Thermo Fisher CetaD, and Thermo Fisher Falcon III to SMV crystallographic format (*.img)
a software package for comprehensive analysis of hydrodynamic data from analytical ultracentrifugation experiments.
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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.
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(Visualization Tool Kit) 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.
a set of command line tools for sequence logo generation.
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.
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an interactive image manipulation program for the X Window System that operates 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 (with ghostscript version 2.6 or above) it can also display them.
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