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Computational Biology→Resources: Software Links

Software Links for Computational Biology*
  • Avogadro
    Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.

  • AutoDock
    AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.Current distributions of AutoDock consist of two generations of software: AutoDock 4 and AutoDock Vina. AutoDock 4 actually consists of two main programs: autodock performs the docking of the ligand to a set of grids describing the target protein; autogrid pre-calculates these grids. In addition to using them for docking, the atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders. AutoDock Vina does not require choosing atom types and pre-calculating grid maps for them. Instead, it calculates the grids internally, for the atom types that are needed, and it does this virtually instantly.

  • Bioconductor
    Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development.

  • BioModels Database
    BioModels Database is a repository of computational models of biological processes. It hosts models described in peer-reviewed scientific literature and models generated automatically from pathway resources (Path2Models). A large number of models collected from literature are manually curated and semantically enriched with cross-references from external data resources (such as publications, databases of compounds and pathways, ontologies, etc.). The resource allows scientific community to store, search and retrieve mathematical models of their interest. In addition, features such as generation of sub-models, online simulation, conversion of models into different representational formats, and programmatic access via web services, are provided.

  • Bioclipse

  • BioRails

  • BALL
    Rapid Software Prototyping can significantly reduce development times in the field of Computational Molecular Biology and Molecular Modeling. BALL (Biochemical ALgorithms Library) is an application framework implemented in C++ that has been specifically designed for this purpose. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization .

  • BioMoby
    The MOBY system for interoperability between biological data hosts and analytical services The MOBY-S system defines an ontology-based messaging standard through which a client will be able to automatically discover and interact with task-appropriate biological data and analytical service providers, without requiring manual manipulation of data formats as data flows from one provider to the next.

  • BioJava
    BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

  • BioPerl
    The Bioperl Project is an international association of users & developers of open source Perl tools for bioinformatics, genomics and life science

  • BioPHP
    PHP for Bioinformatics

  • BioRuby
    BioRuby comes with a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, for the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.

  • Biopython
    Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.

  • Computational Resources for Drug Discovery
    CRDD (Computational Resources for Drug Discovery) is an important module of the in silico module of OSDD. The CRDD web portal provides computer resources related to drug discovery on a single platform.

  • Database for Annotation, Visualization and Integrated Discovery (DAVID )
    DAVID now provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

  • EMBOSS (European Molecular Biology Open Software Suite)
    EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.

  • Gene Designer

  • GenMAPP (Gene Map Annotator and Pathway Profiler)

  • GENtle
    GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more.

  • GenePattern
    GenePattern provides hundreds of analytical tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry, and network analysis. These tools are all available through a Web interface with no programming experience required.

  • Handel

  • Integrated Genome Browser (IGB)
    IGB is a fast, free, and highly customizable genome browser you can use to view and explore big genomic datasets. IGB runs on your desktop and can load data from your local files and also from the internet.

  • JAligner
    An open source Java implementation of the Smith-Waterman algorithm with Gotoh's improvement for biological local pairwise sequence alignment using the affine gap penalty model.

  • KNIME
    KNIME Analytics Platform is the open source software for creating data science. Intuitive, open, and continuously integrating new developments, KNIME makes understanding data and designing data science workflows and reusable components accessible to everyone.

  • LabKey Server
    LabKey Server lets you bring data together from multiple sources into one repository. These sources can be physically separated in different systems, such as data in Excel spreadsheets, different databases, FreezerPro, REDCap, etc. Or the data sources can be separated "morphologically", having different shapes. For example, patient questionnaires, instrument-derived assay data, medical histories, and specimen inventories all have different data shapes, with different columns names and different data types. LabKey Server can bring all of this data together to form one integrated whole that you can browse and analyze together.

  • MassWiz

  • MEGA
    The objective of the MEGA software has been to provide tools for exploring, discovering, and analyzing DNA and protein sequences from an evolutionary perspective.

  • MEGAN
    MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools you need in one application.

  • PyMOL
    PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.

  • QuteMol
    QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilites through OpenGL shaders to offers an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins.

  • Snagger

  • The Genomic HyperBrowser
    The GSuite HyperBrowser system includes a range of tools to handle acquisition, processing and analysis of collections of genomic tracks, represented in a simple tabular format, GSuite. Please proceed in either basic or advanced mode.

  • Taverna
    Taverna is an open source and domain-independent Workflow Management System – a suite of tools used to design and execute scientific workflows and aid in silico experimentation.

  • TREEFINDER
    TREEFINDER computes phylogenetic trees from molecular sequences.

  • UGENE
    UGENE is free open-source cross-platform bioinformatics software It works perfectly on Windows, macOS and Linux

  • Utopia

  • xrate

  • AlleleID
    AlleleID is a comprehensive desktop tool designed to address the challenges of bacterial identification, pathogen detection or species identification. With ClustalW multiple sequence alignment at its core, AlleleID can be used to design species identification/cross species probes for microarrays or real time PCR including SYBR Green, TaqMan MGB, TaqMan probes, Molecular Beacons and real time PCR primers. AlleleID also offers support for designing microarray experiments for detecting alternative splicing events.

  • Archaeopteryx
    Archaeopteryx is a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees. Archaeopteryx (the successor to ATV) is entirely written in the Java programming language (it is based on the forester libraries). It can be used both as applet (ArchaeopteryxA and ArchaeopteryxE) and as a standalone application.

  • Arlequin
    An Integrated Software for Population Genetics Data Analysis

  • Biskit
    Biskit is a modular, object-oriented Python library for structural bioinformatics research. It facilitates the manipulation and analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories. For efficient number crunching, Biskit objects tightly integrate with numpy (Numeric Python). Biskit also offers a platform for the rapid integration of external programs and new algorithms into complex workflows. Calculations are thus often delegated to established programs like Xplor, Amber, Hex, DSSP, Fold-X, T-Coffee, TMAlign and Modeller; interfaces to further software can be added easily. Biskit also simplifies the parallelisation of calculations via PVM (Parallel Virtual Machine).

  • BioModels
    BioModels is a repository of mathematical models of biological and biomedical systems. It hosts a vast selection of existing literature-based physiologically and pharmaceutically relevant mechanistic models in standard formats. Our mission is to provide the systems modelling community with reproducible, high-quality, freely-accessible models published in the scientific literature.

  • Beacon Designer
    Beacon Designer automates the design of real time primers and probes. It is used by molecular biologists worldwide to design successful real time PCR assays. It saves the time and the money involved in failed experiments. Beacon Designer is a flexible solution to your real time primer and probe design needs and pays for itself many times over.

  • BioExtract Server
    BioExtract harnesses the power of online informatics tools for creating and customizing workflows. Users can query online sequence data, analyze it using an array of informatics tools (web service and desktop), create and share custom workflows for repeated analysis, and save the resulting data and workflows in standardized reports.

  • BioSLAX
    BioSLAX is a new live CD/DVD suite of bioinformatics tools that has been released by the resource team of the BioInformatics Center (BIC), National University of Singapore (NUS). Bootable from any PC, this CD/DVD runs the compressed SLACKWARE flavour of the LINUX operating system also known as SLAX.

  • Clone Manager
    Clone Manager Professional provides a comprehensive, fully integrated set of tools for enzyme operations, cloning simulation, graphic map drawing, primer design and analysis, global and local sequence alignments, similarity searches, and laboratory-sized sequence assembly projects. You can also use Clone Manager as a quick and easy way to view or edit sequence files, find open reading frames, translate genes, find genes or text in files, or use primer or sequence phrase collections.

  • Cn3D
    Cn3D ("see in 3D") is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez Structure database. Cn3D is provided for Windows and Macintosh, and can be compiled on Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features. (For those who prefer to view 3D structures on the web, without the need to install a separate application, iCn3D ("I see in 3D") is available as of April 2016.)

  • Coot (Crystallographic Object-Oriented Toolkit)
    Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, skeletonization, non-crystallographic symmetry and more.

  • Clustal: Multiple Sequence Alignment
    Multiple alignment of nucleic acid and protein sequences

  • CS-BLAST (Context-Specific BLAST)
    CS-BLAST is a tool that searches a protein sequence that extends BLAST using context-specific mutation probabilities.

  • Cytoscape
    Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization.

  • Dendroscope
    An interactive viewer for rooted phylogenetic trees and networks

  • DIALIGN-TX
    DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. DIALIGN-T is a reimplementation of the multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly better alignments on locally and globally related sequence sets than previous versions of DIALIGN. However, like the original implementation of the program, DIALIGN-T uses a a straight-forward greedy approach to assemble multiple alignments from local pairwise sequence similarities. Such greedy approaches may be vulnerable to spurious random similarities and can therefore lead to suboptimal results. In this paper, we present DIALIGN-TX, a substantial improvement of DIALIGN-T that combines our previous greedy algorithm with a progressive alignment approach.

  • FASTA
    The FASTA programs find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.

  • FoldX
    FoldX provides a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes. The predictive power of FoldX has been tested on a very large set of point mutants (1088 mutants) spanning most of the structural environments found in proteins. FoldX uses a full atomic description of the structure of the proteins.

  • Galaxy
    Galaxy is an open source, web-based platform for data intensive biomedical research.

  • Geneious
    Geneious provides intuitive visualization tools and advanced analytics capabilities that help you extract detailed, precise antibody sequence information. Screen, investigate, and compare your analysis results and upload and manage experiment data.

  • Genevestigator
    GENEVESTIGATOR is a high performance search engine for gene expression. It integrates thousands of manually curated, well described public microarray and RNA-Seq experiments and nicely visualizes gene expression across different biological contexts such as diseases, drugs, tissues, cancers, cell lines or genotypes. The high diversity of curated experiments allows GENEVESTIGATOR to project your genes or your data against a broad spectrum of reference profiles and datasets.

  • GENSCAN
    Algorithm for ab initio prediction of complete gene structures in vertebrate, Drosophila and plant genomic sequences

  • HMMER
    HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). HMMER is often used together with a profile database, such as Pfam or many of the databases that participate in Interpro. But HMMER can also work with query sequences, not just profiles, just like BLAST. For example, you can search a protein query sequence against a database with phmmer, or do an iterative search with jackhmmer.

  • Jalview
    Jalview is a free program for multiple sequence alignment editing, visualisation and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.

  • MAFFT
    MAFFT is 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), etc.

  • MochiView
    MochiView is Java software that integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis. It is a pure Java desktop application that is easy to use and that can produce data and plots that are easily exportable for publication or analysis with other programs.

  • MODELLER
    MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (3,4), and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.

  • MUMmer
    MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.

  • NoeClone
    NoeClone provides a knowledge-enhanced and comprehensive solution for virtual cloning, gel simulation, plasmid map drawing and sequence analysis. NoeClone transforms the complex molecular cloning process into a pleasant working experience. Empowered with versatile functionalities of NoeClone, molecular biologists can truly enjoy the fun of molecular manipulation and DNA design in silico.

  • OLIGO
    OLIGO Primer Analysis Software is the essential tool for designing and analyzing sequencing and PCR primers, synthetic genes, and various kinds of probes including siRNA and molecular beacons. Based on the most up-to date nearest neighbor thermodynamic data, Oligo's search algorithms find optimal primers for PCR, including TaqMan, highly multiplexed, consensus or degenerate primers. Multiple file batch processing is possible. It is also an invaluable tool for site directed mutagenesis.

  • PAUP
    Phylogenetic Analysis Using PAUP

  • Phyloscan
    Phyloscan is a free web server that scans mixed aligned and unaligned DNA sequence data for statistically significant instances of a user-supplied pattern / motif.

  • phyloXML (XML for evolutionary biology and comparative genomics)
    phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly used features, such as taxonomic information, gene names and identifiers, branch lengths, support values, and gene duplication and speciation events. Using these standardized elements allows interoperability between various applications and databases. Furthermore, both due to extensible nature of XML itself and the provision of elements by phyloXML, extensibility as well as domain specific applications are ensured. The structure of phyloXML is described by XML Schema Definition (XSD) language.

  • Primer Premier (A Comprehensive PCR Primer Design Software)
    Primer Premier's search algorithm finds optimal PCR, multiplex and SNP genotyping primers with the most accurate melting temperature using the nearest neighbor algorithm. Primers are screened for secondary structures, dimers, hairpins, homologies and physical properties before reporting the best ones for your sequence, in a ranked order.

  • PrimerPlex
    PrimerPlex is an efficient & sophisticated tool for designing primers for multiplex PCR. Multiplex assays facilitate amplification of multiple targets in a single reaction vessel, reducing both, the time and cost of experimentation.

  • PROTOMAP
    PROTOMAP is a recently developed technique to map in vivo substrates of proteolytic events. PROTOMAP uses 1D SDS-PAGE and mass spectrometry to globally identify shifts in gel-migration and corresponding changes in the topography of proteolytic fragments. In 2008, PROTOMAP was used to study the intrinsic apoptosis pathway in Jurkat T-cells, and these experiments identified many proteins known to be cleaved during apoptosis, as well as hundreds of novel caspase substrates. More-recently, an advanced quantitative variant of PROTOMAP was developed that utilizes SILAC for precise quantitation, and incorporates detected sites-of-phosphorylation into the topographical maps of proteins (peptographs). This new method, called quantitative phosphoPROTOMAP (or qP-PROTOMAP) permits the isoform-specific identification and quantification of phosphorylation sites and provided the first global picture of phosphorylation dynamics during apoptosis.

  • PSORT
    PSORT is a computer program for the prediction of protein localization sites in cells. It receives the information of an amino acid sequence and its source orgin, e.g., Gram-negative bacteria, as inputs. Then, it analyzes the input sequence by applying the stored rules for various sequence features of known protein sorting signals. Finally, it reports the possiblity for the input protein to be localized at each candidate site with additional information.

  • PupaSuite
    Program to calculate accurate MW and pI values from proteins considering the effects of post-translational modifications. Results are displayed as calculated values of pI and MW for each protein and are also plotted on two-dimensional (2D) gel images.

  • PEAKS
    PEAKS software is a comprehensive, vendor-neutral, proteomics tool to provide systematic identification and quantification of peptides/proteins in a complex protein mixture using tandem mass spectrometry (LC-MS/MS). With PEAKS, directly load in the raw LC-MS/MS data from the mass spectrometer (no need to convert the data first), and select from PEAKS workflows to perform peptide and protein identification (such as de novo sequencing, database and spectral library searching), PTM and mutation characterization, and quantification. The interactive interface also provides a detailed, easy-to-use, user interface for data visualization, result validation and reporting.

  • RasMol
    RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle. RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on wide range of architectures and operating systems including Microsoft Windows, Apple Macintosh, UNIX and VMS systems. UNIX and VMS versions require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The X Windows version of RasMol provides optional support for a hardware dials box and accelerated shared memory communication (via the XInput and MIT-SHM extensions) if available on the current X Server.

  • Soaplab2
    Soaplab2 (or Soaplab) is a tool that can automatically generate and deploy Web Services on top of existing command-line analysis programs. It is especially well suited for applications with well described input and output parameters, such as EMBOSS (a package of Open Source software for sequence analysis). Soaplab allows integration of many applications within a single programming interface.

  • SplitsTree4
    SplitsTree4 is the leading application for computing evolutionary networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks.

  • Stemloc
    Stemloc is a program for multiple alignment of RNA using Stochastic Context Free Grammars. Stemloc uses "alignment envelopes" and "fold envelopes" to simultaneously constrain both the alignment and the secondary structures of the sequences being compared, rendering the RNA comparison problem tractable on commodity hardware.

  • T-Coffee
    A collection of tools for computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.

  • UCSF Chimera
    UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, nonprofit, and personal use.

  • WHAT IF
    [WHAT IF] is a versatile molecular modelling package that is specialized on working with proteins and the molecules in their environment like water, ligands, nucleic acids, etc.

  • YASS
    YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). Like most of the heuristic pairwise local alignment tools for DNA sequences (FASTA, BLAST, PATTERNHUNTER, BLASTZ/LASTZ, LAST ...), YASS uses seeds to detect potential similarity regions, and then tries to extend them to local alignments. This genomic search tool uses multiple transition constrained spaced seeds that enable to search more fuzzy repeats, as non-coding DNA/RNA.


*Disclaimer: The software listed above are for information purpose only and csfreelist has nothing to do with these software and their respective organizations. We DO NOT guarantee about the correctness, perfectness, flawlessness, etc. of the information provided on this webpage and on other information-purpose webpages of this website. For the contents of Third party websites / resources, we take absolutely no responsibility. The software which are free are conditionally free and available with terms & conditions established by their developers and other concerned persons / organizations. For exact terms & conditions, please visit their websites and /or contact them.

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