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    A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

    - 3 -
  • 3D Ribosomal Modification Maps Database

  • - A -
  • ABCC Genome Annotation Project (empty)
  • ABE: A bioassay analysis program
    ABE is a small, fast and convenient program for visualizing and modeling experimental bioassay data. The data can be modeled using either polynomials or a more specific four-parameter model based upon the standard, sigmoidal dose-response curve.
  • Chromatogram file
  • AbifTake (empty)
    A python module for parsing ABI trace file (and hopefully ABI gel file too in the not-so-distant future).
  • AcE: Gene finding accuracy evaluation
    Gene finding accuracy evaluation tool and test datasets. It allows a nearly complete set of evaluation statistics to be easily generated on a customisable set of test sequences. AcE has nothing to do with ACEDB. You can download the program '' an
  • Advaitha (empty)
  • ALiBio: Biolibrary for C++
    A C++ library of efficient algorithms for bioinformatics
  • AlignNemo
  • Alkahest: High-throughput (empty)
    Alkahest is an initiative to produce free open source software systems for high-throughput DNA sequence data management and analysis.
  • AminoNet : Amino Acid Network
    Aminonet tool takes pdb file as input form local machine or from and calculates different parameters of the network. Using AmonoNet one can visualize the network in an interactive way.
  • Ampred
    Welcome to Ampred server,which predicts the Antimicrobial activity of given sequence. The activity may be antifungal, antiviral and antibacterial .This server works based on Multidimensional signatures of antimicrobial peptides (Yount and Yeaman.2004).
  • Amrita Bio-Informatics Society (empty)
  • Analytical Chemists in food (empty)
  • ANEX: Alignment Neighborhood EXplorer
    This group provides ANEX(_P), a program package to compute probability distributions of alternative MSAs by exploring neighborhoods of an input MSA. The probabilities are computed under genuine sequence evolution models with realistic indels. (FTP only)
  • AnnHyb: Nucleotide sequence management
    AnnHyb is a free software for working with and managing nucleotide sequences in multiple formats. Features include sequence annotation, restriction analysis, pattern searching, retrieval from servers, etc.
  • AnovArray: anova of gene expression
    AnovArray is a set of SAS macros for the Analysis of Variance of Gene expression. It can be applied to the quantification of biological and technological variation and to the identification of differentially expressed genes in two or more conditions.
  • ANTHEDNA (empty)
    ANTHEDNA is a package of integrated UNIX freeware tools for retrieving and analyzing sequence data. It is called ANTHEDNA because it was developed for analyzing the DNA sequence data obtained from the ribosomal database project.
  • Antisense Database (empty)
  • antisenseML
    AntisenseML integrate sufficient information to provide fast, flexible access to the data. Moreover,XSLT transformation was made to render the antisenseML file into HTML view.Some useful tools to create update antisenseML will be released soon
  • AntPred (empty)
  • Application Validation Documents
    These documents may be useful as examples to help validate your application in compliance with FDA GxP regulations.
  • ARGO: Antibiotic Resistance Gene Online
    ARGO (Antibiotic Resistance Genes Online) is intented to be a comprehensive web Resource for Scientists, Clinicians and other people who are interested in the looming problem of rise and spread of antibiotic resistant pathogens worldwide.
  • Array-A-Lizer: Microarray analyzer
    Please visit to see our website and for a detailed description of Array-A-Lizer - A serial DNA microarray quality analyzer. Executables and sourcecode of the project are also available at the website.
  • Asap: A framework for promoter analysis
  • ASID: Arabidopsis System Interaction D/B
    We have derived novel clustering algorithm taking into consideration certain biological assumptions like conditional coregulation and properties of microarray data, uploaded at website Gene can be queried (only for Carbohydrate).
  • Assemble: a tool to construct and study RNA architectures
  • Assessment of Co-Evolution Software
    A group dedicated to facilitating co-evolution analysis of proteins and/or nucleic acids. Provides open-source, user friendly software to allow researchers with little bioinformatic or programming experience to determine co-evolution in molecules of inter
  • Asterias
    Asterias is a set of web applications for the analysis of genomic (and, to a lesser extent, proteomic) data that cover from data normalization to development of prediction models for survival data.
  • Atlas: Integrated database project
    The Integrated Database Project is an effort to integrate multiple forms of biological, publication and ontological data under one query space for data mining. At its core sit relational databases whose tables model the data structure of the information.
  • AYURVEDA: Virtual drug develop. (empty)
    We are developing obesity control drug form taditional inadian medicinal plants, becouse medicines from plants have less side effects compare to allopathy medicines
  • Ayurvedic database (empty)

  • - B -
  • Balony
  • Barjis Petrinet Lab (empty)
  • Base Pad
    This is a windows based base sequence editor. Search, complement, XNA to amino acid,amino acid to XNA,3 to1 & 1to 3 letter code, invert, find ORF,statistics of bps,2bp palindromes
  • BatCave
    The BatCave will be an integrated database that allows end users to navigate and visualise their methylation data with ease, specifically data generated by the programme 'Batman' (Bayesian Tool for Methylation Analysis).
  • Bayallele: Genetic data analyzer
    Bayallele is a Java-based application that uses bayesian inference and markov chain monte carlo methods to analyse genetic data. The analysis revolves around obtaining separate estimates of population size and migration rate for the sampled populations
  • Bayesian Model Averaging for genomics / transcriptomics data
  • BCTool: a biclustering comparison toolbox
  • Bertone Group
  • BhambriBII and Underscores (empty)
  • BIC CHOP (empty)
  • BIC-INDORE (listed)
  • BicAT Plus: Biclustering method comparisons
  • Bifx Free Software Builds (empty)
  • Binosys Technologies (empty)
  • Bio-Informatics Tutorial
    A nascent tutorial on bio-informatics, currently covering molecular biology basics and advanced topics like genomics. The project files will be updated every fortnight (2 weeks). Contributions welcomed.
  • BIO-INNOVATORS: osteoporosis (empty)
  • Bio-Linux: Linux for Biologists
    Bio-Linux 8 is a powerful, free bioinformatics workstation platform that can be installed on anything from a laptop to a large server, or run as a virtual machine. Bio-Linux 8 adds more than 250 bioinformatics packages to an Ubuntu Linux 14.04 LTS base.
  • BIO-NIX: A Linux OS distribution (empty)
  • Bio-toolkit
  • Bio-Wave: Wavelet toolkit (empty)
    Bio-Wave is a Wavelet based semantic pattern & relation extractor and visualizer. It can be used for sequencing, pattern recognition, curve fitting and other similar processes, especially in gene sequencing and tissue viz. problems.
  • Bio/Chem-Informatics Center
  • BioBanner Ad Network
  • BioBaseStation (empty)
    Project Definition: Development of computational tools such as algorithms, software and databases for the collection, interpretation and dissemination of the vast quantities of complex mapping and sequencing data that are generated by human genome res
  • BioBrew: Package repository
    BioBrew is a collection of open-source applications for life scientists and an in-house project at Bioinformatics.Org.
  • BioBrowser (empty)
    BIOBROWSER is a portal to the existing bioinformatics universe. It encompasses in itself hyperlinked nodes to all major nucleotide, RNA, Protein sequences along with structural and genomics databases to name a few. Also links major related servers.
  • BioC#: Biolibrary for C#
    The BioC# Project is an open-source project dedicated to providing C# tools for processing biological data. The BioC# library will provide a foundation upon which both free software and commercial packages can be developed.
  • Biochemical Algorithms Library (listed)
    BALL (Biochemical Algorithms Library) is an application framework 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, comparis
  • Bioclues
  • BioCocoa: Biolibrary for Obj-C
    BioCocoa is an open source OpenStep (GNUstep/Cocoa) framework for bioinformatics written in Objective-C. We intend to provide OpenStep programmers with a full suite of tools for handling and manipulating biological sequences.
  • BioECMA (empty)
  • Biogress: PostgreSQL for (empty)
  • Bioinformatics Algorithms Research
  • Bioinformatics analysis at UNICZ.IT
  • Bioinformatics and Computational Biology at ISA-CNR, ITALY
  • Bioinformatics Benchmarking System
    The Bioinformatics Benchmark System is an attempt to build a reasonable testing framework, tests, and data, to enable end users and vendors to probe the performance of their systems.
  • Bioinformatics database search (empty)
  • Bioinformatics Education (empty)
  • Bioinformatics for Bioremediation
  • Bioinformatics Needs Assessment Group
    SERVING the bioinformatics requirements of experimentalists. DEFINING best practice. PROMOTING basic training. PROVIDING a service.
  • Bioinformatics Software Testing (empty)
  • Bioinformatics System Dynamics (empty)
    This is a unique project that tries to make an informatic simulated system from a genetic /physiology well-known system.
  • BioInformatics Workbench (empty)
    This project aims to create a list of functional requirements and technical specifications (flowcharts, classdiagrams, etc.) for the development of a complete workbench solution created in .NET/C# for researchers, students and others who are interested.
  • Bioinformatist Wiki
  • Bioinfozilla : Firefox extension for bioinformatics
  • Bioinsilico:Drug target database (empty)
  • BioJafa (empty)
  • bioLegato - general purpose graphic user interface
    bioLegato is a programmable graphic interface capable of handling a wide range of data types. Each bioLegato is an "Object". The canvas area allows the user to view and manipulate the data. The menu area runs external programs, which correspond to the met
  • BioLet: Wavelet analysis tools (empty)
    Bioinformatics tools for performing wavelet analysis on DNA sequences
  • BioLib: Biolibrary for FORTRAN
    In order to avoid re-inventing the wheel, a collection of FORTRAN code that may be useful for your scientific program.
  • BioLore: A knowledgebase (empty)
  • BIOMAP Project (listed)
  • Biometrical Methods (empty)
  • bioNMF: NMF in Biology
  • BioPHP: Biolibrary for PHP
    This BioPHP project aims to develop modules and, eventually, sample applications for bioinformatics in PHP both for web AND standalone applications (PHP's utility outside of the web is often overlooked.)
  • BioQuery: Search strategies (listed)
    BioQuery provides a single, powerful user interface for building search strategies to multiple biomedical databases, and provides a full update service that sends you new data matching your search criteria when new entries are added to the databases.
  • Bioscys (empty)
    promote the knowledge and application of bioinformatics in third world countries
  • bioseg
    BIOSEG is a biological interval type for PostgreSQL. A PostgreSQL GiST index is used to improve the speed of overlap, contains and contained-in queries. Note: This project is now un-mantained as PostgreSQL 9.2 and later include a built in range type.
  • BiOSoA (empty)
  • biosql on rails (empty)
  • BioSuite (empty)
  • BioSVG
  • BioVM: Bioinformatics Virtual (empty)
  • BIRCH: Comprehensive bioinfo. system
    BIRCH bundles together many of the most commonly-used bioinformatics programs, unified through a graphic interface. BIRCH is designed to simplify the task of managing a bioinformatics core facility, but can also run on a single PC.
  • blast2malign: Multiple seq. alignment
    An easy to use script that creates a multiple alignment (relative to the query) from the database hits of a BLAST search. Multiple HSPs from a database sequence are combined or separated depending on their relationship to each other.
  • blast2ps: Graphical overview of output
    Fast and easy to use script producing a graphical overview of blast results.
  • BLASTometer: Monitor BLAST jobs
  • Blaxter Lab (empty)
  • BLGM
    BioLinux Goes Mobile
  • BLISS Genetics Project: Genetics, Psychology, Spirituality
  • Blogo: Display biological sequence bias
    Blogo is intended to be a kind of sequence logo generator that detects and displays biological position-specific sequence bias with reduced background noise.
  • BNA: Biological Network Analysis
  • BranchClust: Assembly of Gene Families
    A perl script that assembles families of orthologous genes by parsing a phylogenetic tree reconstructed from a mixture of orthologs and paralogs for a set of n taxa. Given a tree as input, the script reports families of orthologs, and it lists in- and out
  • BSQuery (empty)
    BSQuery 1.0 desktop utility that can be used to instantly retrieve sequence annotations from GenBank and other documents (e.g. AGAVE, etc),regardless of the document?s location (a local computer, LAN-based server, online, etc)
  • BTL: Biomodeling library for C++
    The BTL provides generic mathematical components that allow C++ programmers to more rapidly construct applications that model biological entities.

  • - C -
  • C2Analyzer : Cotargeted Cofunctional Analyzer
  • Calcium binding protein predictor
    CalPred is a "tool for EF-hand calcium binding protein prediction and calcium binding region identification" using machine learning techniques. It is a free web based software package and is accessible via world wide web from various platforms.
  • Cancer (empty)
  • Cancer genome architecture effects on lineage selection
    The project "Cancer genome architecture effects on lineage selection" analyses the constraints of the genome architecture on somatic cancer evolution. It can be considered an analogy to the concept of “evolvability” in Darwinian species evolution.
  • Cancer Journalist's View
  • Cardiovascular genes database (empty)
    Cardiovscular Gene Database provide you with VISTA system for the investigators in the Cardiovascular biology and pharmacology community.
  • Career Center
  • CAT-O: Concatenate Orthologous Sequences
    CATCH is an tool for exploring patterns in ChIP profiling data. The CATCH algorithm performs a hierachical clustering of the profile patterns with an exhaustive alignment at each step. The tool has a user-friendly graphical interface.
  • CBESW: Sequence Alignment on the PS3
  • CD-HIT: Sequence clustering software
    CD-HI/CD-HIT clusters protein sequence database at high sequence identity threshold. This program can remove the high sequence redundance efficiently. Program written by: Weizhong Li
  • CEBIB Discussion Group
  • CELUTIL: Cel file utility
    Celutil is an utilty to read&write, compare, convert, query Affymetrix CEL file in binary & ASCII format, gzipped or not. Celutil is a linux command line written in C++ and should compile and run on windows, MacOsX. Based on Affy File parsers & zlib.
  • CGView
  • ChemChains: Simulation & analysis of logical models
  • Chemical Comparator
  • ChemIsosteres: A Structure-Based Bioisosteres
  • Chinook: P2P system using JXTA (listed)
  • Chromhome: Comparative genomics DB
    Chromhome ( is a database of comparative genomics showing maps of chromosome homologies across species.
  • CiteMan
  • ckr5 protein protein interaction (empty)
  • Clinical Data Management Group (empty)
  • Clusterfunc: Clustering of functional categories
  • CMView - Protein Contact Map Visualisation and Analysis
    CMView is a software tool written in Java which provides functionality for viewing, analyzing and modeling protein contact maps.
  • Codon Usage Analyzer
    A web-based program that processes and displays information from the Codon Usage Database in an easy-to-read format. Analyze which codons your organism likes to use.
  • Coffee Mug: Hypertension genomics
    WE strive to provide simple solutions for everyday life in a molbio lab
  • COMBOSA3D: Molecule coloring
    A web-based program for comparing sequence conservation patterns to three-dimensional structures.
  • Comparitive Genome Browser (empty)
  • compLED
  • Composition Analysis Toolkit
  • Computational Thinking in Life Sciences
  • Corynebacterium diphtheriae NCTC13129 Re-annotation
  • CRAIG (empty)
  • CRISPR: a resource for CRISPR guideRNA design
  • CRNPRED: 1D protein structure prediction
    A program to predict secondary structures, contact numbers, and residue-wise contact orders of native protein structures from amino acid sequence. This program is based on the critical random networks method.
  • CS Miner
  • Cyntenator: Progressive gene order alignments
    Cyntenator is a software for identification of conserved syntenic blocks between multiple genomes.
  • Cyprus Visioneers Group (empty)

  • - D -
  • Database of Antibiotics (empty)
  • DBBP: BioPython tools (empty)
  • dChip: Gene Expression and SNP Genotyping
  • Delila-Genome: Protein binding analysis
    A Linux-based system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by scanning genomic sequences with information theory-based (or user-defined) weight matrices.
  • DeltaStat: 2D gel analysis
    DeltaStat performs statistical calculations on data from 2D gel experiments quantified in Delta2D. DeltaStat combines the power of R with the efficiency of a database to handle the large amounts of data generated in proteomics experiments.
  • Dengue Drug Target Database
  • DENSERM: DEtecting Negative SElection on Recurrent Mutations
    This project aims to develop programs to DEtect Negative SElection on Recurrent Mutations. Currently, it provides a package, DENSERM_P (version 0.3), which consists of Perl scripts and modules, aided by several shell scripts. Available at FTP repository.
  • DEODAS: For degenerate oligos (listed)
    A GNU/Linux-based system, called DEgenerate Oligonucleotide Design & Analysis System (DEODAS), for designing and electronically analyzing consensus-degenerate oligonucleotides is being developed by integrating published software tools from other authors.
  • DIP4FISH: Telomere analysis tools
    Providing tools for QFISH using free software (macros for NIH image) with examples of processed images; methods to calculate mean TRF length by southern blot with image processing and source code of macro for densitometry; and presentations
  • Disperse
    Software and data for design of selector assays for targeted resequencing applications. The software is a Java and Perl pipeline that performs the tasks required to design selector probes for the coding regions of a set of target genes.
  • Distributed Computing Power Proj (empty)
  • DNACGR: D/RNA pattern visualization
    Program to visualise patterns in DNA and RNA by using Chaos Game Representation
  • DNALinux: Bioinformatics Virtual Machine
    A Xubuntu Linux based virtual machine Bioinformatics environment.
  • DrugGenesis: Avian influenza DB (empty)
  • Dynamic Lab Notes

  • - E -
  • E-CELL Simulation Environment Version 2
    This is portable and stable branch of the E-CELL project. Linux, Solaris, and MS-Windows versions are under developping. You will be able to run ecell2 not only in interactive mode but also in batch mode.
  • EasyBioDB: a pipeline for biodatabases
  • EasyBlast
  • Ebbie: Small RNA analysis and storage
  • EcoBio SOAP Software Solution
    Tools in Measuring, Monitoring and Analysing Bio-Diversity. The project's goal is to study software solutions that will aid and will be used to find, visualize, analyze the information and most importantly, communicate it to other people around the globe
  • EmblEx
    EmblEx is a tool to retrieve subsequences as defined by complex descriptors in the Features qualifiers of the EMBL entries (ASCII files). Users can define complex keywords (or regular expressions) to be searched for. Many outputs are also possible.
  • EnzymeLab (empty)
    EnzymeLab is a program for the numerical and graphical analyses of enzyme kinetics data: the Micaelis-Menton parameters, inhibitor studies (both linear and non-linear), reaction rate/order and mechanism, and assay development/validation.
  • Epistatic MAP Imputation
    Epistatic MAPs(E-MAP) are a high-throughput approach capable of quantifying aggravating or alleviating genetic interactions between gene pairs. This project contains applications for imputing / predicting missing values in E-MAP datasets.
  • ESPSim
    ESPSim is an open source JAVA application designed to compute the similarity of protein electrostatic potential maps.
  • Excel2SVM
  • Expression Signature Patterner (empty)
    ESP is a flexible platform to evaluate the discrimination abilities of user-defined expression signatures. Besides, it offers individual prediction information that could be useful for clinically prognosis and clinical management decisions.
  • eyeLIMS

  • - F -
  • FASIMU: Constrained optimization of metabolic networks
  • Feasibility-based Flux Coupling Analysis (FFCA)
  • File Format Converter Tool (empty)
  • FindtRNA : tRNA Finder
  • FirstGlance in Jmol
    FirstGlance in Jmol is a simple, free, browser-based tool for macromolecular visualization. It easily shows you the main features of any published macromolecular model (PDB file). It runs on all common browsers and platforms.
  • FishermansFriend (empty)
  • (empty)
  • FLIMS: Laboratory workflow (empty)
    FLIMS is reborn. I will be providing small UI components and code snippts that should add up to an application. The general purpose is to build a framework for bioinformatic programming. Maybe hooks into BioRuby and touching on experimental technologies s
  • Fly Phylogenomics Group
    A group of systematic biologists working on using RNAseq transcriptome data to study the phylogeny of flies and different fly groups. Our initial focus is on the parasitic fly family Tachinidae
  • FOG: A tool to Map Genomic Features on to Genes
    FOG can help mapping important genomic features to the latest version of the human genome and also to annotate new features. such as miRNAs, microarray primers or probes, Chip-on-Chip data, CpG islands and SNPs to name a few.
  • Formal Ontology in Biology
  • Format Conversion Tool (empty)
  • FragSize: DNA band size determination
    FragSize is a software tool designed to help molecular biologists in DNA band size determination. It use an graphic user interface, so, use FragSize is very easy. Just load the gel image and make the determinations.
  • FragVLib: Fragment-Based Virtual Library
  • FreeMOL Compilation
    FreeMOL is a compilation of free and open source programs forming a framework for computational chemistry, informatics, structural biology and graphics.
  • fs_kit: Analysis of force spectra
    fs_kit is a force spectroscopy toolbox, containing programs to fit, align and analyze spectra. It is currently a work in progress. The current state is best described as beta version.
  • Functional Annotation of SCOP (empty)

  • - G -
  • G-language Genome Analysis Environment
    G-language GAE is a software package aiming to provide a generic development and analysis environment for the analysis of complete genomes. (Development at is discontinued. Please proceed to the home page at
  • GAG-Binding Proteins Predictor
  • Gautam ORF Finder
    GAUTAM ORF FINDER is a web-based program written in perl script in 2008 to find ORF present in any DNA sequence. User has to just input any DNA sequence i.e. ATGC... and within fraction of seconds the user get desired output.
  • GB-CARTool (empty)
  • gBioSeq: DNA sequence editor for Linux
    gBioSeq is in an early stage of development, but it is already running. The goal is to provide an easy to use software to edit DNA sequences under Linux, Windows, MacOsX, using GTK C# (Mono).
  • gclib: genomic code library and other bioinformatics tools
  • GEMS (empty)
  • Gemvid
    Gemvid is a monitoring system that quantifies overall free movements of rodents without any markers, using a commercially available CCTV and a newly designed motion detection software developed on a GNU/Linux-operating computer.
  • GenBank Creator (empty)
  • Gene aliases disambiguation
  • Gene Cluster with Literature Profiles
  • Gene Duplication (empty)
  • Gene expression compositional assignment (empty)
  • Gene Ontology API for Java
    GO4J is a set of API to manipulate local GO vocabulary. It has four features: parsing four kinds of GO defintion; organize all GO ids with directed graph; evaluating semantic similarity between any two GO ids; visualizing relations between any ids.
  • Gene Ontology Browsing Utility (empty)
  • Gene Prediction Data Consortium
    Data sets for training gene-finding software.
  • Gene Wiki
  • GeneCite: Literature and pathway mining
    GeneCite permits users to specify sophisticated sets of queries and generates a table of the number of citations found for each query. The table can be presented as a web page or in standard spreadsheet format.
  • GeneGnome: Enzyme network builder
    GeneGnome will allow users to build, in the GUI, nodular models of linked cellular enzyme networks in a GNOME environment with the goal of using the underlying calculational engine linked to the GUI to help make testable predictions in real cells.
  • GenePicker (empty)
    Gene Picker is a tool that is developed to display Genetic Information in an easy to use graphical format. The objective is to enable the scientist to access Genetic information archived in a back end database through a graphical representation. This woul
  • Genes Interactions Simulation (listed)
    Gints aims at the simulation of regulation networks.
  • GeNetDB: Regulatory networks platform
    GeNetDB, contraction of Genetic Network Database, is a bioinformatic platform destined to the study of genetic regulatory networks. It contains in one place the data and the way to study them, providing the user an access to all tools needed for his work.
  • Genetic Data Analysis Library
    The Genetic Data analysis Library (GDL) is a dynamic library consisting of a large panel of low-level functions in C for performing various statistical analyses of data from quantitative genomics and genetics.
  • Genetical addressing open (empty)
  • GeneVenn: Gene list Venn Diagram generat
    This Program has a core PHP function that generates venn diagrams, with user input as gene lists, through html forms using java script
  • GenLux: Structural organization of genes
    GenLux is a project focused on the structural organisation of genes, e.g. promoters, splice-sites, etc. To elucidate certain aspects and verify data, modules (written in PERL, Java, etc) are released and put together in a "construction-set"-fashion.
  • Genome ARTIST: ARtificial Transposon Insertion Site Tracker
  • Genome Assembly Script (empty)
  • Genome Assembly Study Group
    I think there is a need of a open forum especially made for genome assembly people so that we can share the knowledge with the world.
  • Genome Cytological Information Server
  • Genome Display Tool
  • Genomic Re-Annotation Tool (empty)
  • Genopolis database codebase
    This this the codebase for the Genopolis Gene Expression database ( It is presented here for futher puplic development or as a resource for similar projects.
  • Genpak: Sequence manipulation tools
    Genpak is a set of simple tools for manipulation of nucleic and protein sequences, written in ANSI C. The programs are supposed to be small, efective, use the Unix pipe/redirect and have a GUI via WWW/CGI.
  • Genquire: Genome browsing and annotation
    Browsing and Annotation of complete or incomplete genomes. Live GUI-manipiulation of the underlying database (with write access).
  • GFIT (empty)
    Gene Function Identification Tool (GFIT) for post-sequencing analyses. UNIX+PERL enables us to query multi-entries and focus on what we want to see.
  • Ghemical: Molecular modelling
    Ghemical is a molecular modelling package. The graphical user interface is built on GTK2. Both quantum-mechanical and forcefield-based methods are supported, and it is also possible to add new methods.
  • GIPSy: Genomic Island Prediction Software
    A Java-based Genomic Island Prediction Software which improves the previously developed Pathogenicity Island Prediction Software (PIPS) by performing other GEI analyses and providing a user-friendly graphical interface. Please, read the Manual.
  • GlutamineBase (empty)
  • GO2MSIG gene set generator
    Produce Gene Set Enrichment Analysis (Broad Institute - GSEA) compatible hierarchical GO based gene sets (MSigDB format) using GO project term relationships and gene/GO term association data from multiple data sources.
  • GORx library (empty)
    << Not released any file yet >> GOR-family algorithms for protein secondary structure prediction.
  • GPBlast: Search for homologous/paralogous protein sequences
  • GUI Blast: Python GUI for BLAST
    Graphical User Interface for NCBI Stand alone BLAST. This is aimed to Windows users sice NCBI BLAST is only command line in Windows. But can be also used in UNIX. Requires Python, wxPython and BioPython.

  • - H -
  • HaploCheck (listed)
  • Harwell Informatics (empty)
    under development
  • Helix - chem profiling (empty)
    A novel protein function prediction technique that helps identify the function of a protein when there are no known similar alignments. Calculations are performed without the need for computationally expensive alignment algorithms or databases.
  • HIPPO library (empty)
    << Not released any file yet >> Spatial, 3D distribution of the hydrophobicity around the protein molecule, (M)olecular (H)ydrophobicity (P)otential (MHP) concept, intra- and inter-molecular interaction.
  • HistoCheck (empty)
  • HydrophobicityPlot
    The program calculates a hydrophobicity plot. Several sets of parameters can be used. (under construction)

  • - I -
  • I, Librarian: bibliography manager
    I, Librarian is a tool to build a web-based annotated library of scientific PDF articles. It is suitable for individuals as well as for small collaborative groups, like science labs or departments.
  • IDEAs web platform
    The IDEAs platform is an integration tool for querying and visualising Interactions, Domains, Experimental results and Annotations. It is intended for visualising omics data in context of a network of relationships between biological objects of interest.
  • IIKmTA : Inter and Intra Kingdom miRNA Target Analyzer
  • Illinois Bio-Gtrid
  • Immigrant genes database
    The Immigrant genes database contains genes that have immigrated or been transferred from one species to another. Such knowledge is useful for studies that rely on phylogenetic and/or sequence similarity information.
  • In silico studies for complex diseases
  • In-depth mining of microarray data via hybrid SOM-SVD
  • Integrative Analysis of Clinical and Genetic data (CLIGEN)
  • Ishmael: BioMOBY browser
    Ishmael is a standalone browser for the BioMOBY Biological Web Services system. Source is in CVS.
  • ISPyB PocketSample
    ISPyB Pocket Sample bridges the gap between the Crystalization information system (PIMS, ...) and the Information System for Protein crYstallography Beamlines : ISPyB. It keeps track of samples via datamatrix codes, ...
  • iVUN - interactive Visualization of Uncertain Networks
    iVUN was designed to investigate and analyze system models of biochemical reaction networks as well as the attributes describing the systems behavior. These include outputs, samples of potential parameters, and dynamic samples of fluxes and states.

  • - J -
  • JaMBW: Molecular biology workbench
    Java based Molecular Biologist's Workbench
  • Jannotatix: Sequence analysis system
    Jannotatix is a java-based Sequence and Annotation viewer. It's main purpose currently is to run different motif discovery programs on the sequences, supply the correct parameters and convert the results back to gff-format.
  • Java BioDataPlatform
    A generic framework that could help research groups to design, accesss, search, share, and exchange bio-data. This project trys achieve this goal to help bio-data integration and management for small/middle sized research groups in avoid of purchasing exp
  • Java interface to the M-CL algorithm
  • Java-R-Nova (empty)
    Amaanova analysis in Java is intended to write the amaanova package in Java with interface to R. More bio-statitical module will be ported in this way.
  • Jaypee University of Information Technology
  • JCoast
    Comparative Analysis and Search Tool for prokaryotic genomes. The JCoast package provides a API and GUI that makes use of the standardised genome processing and storage system, GenDB.
  • JDesigner: Biochemical network designer
    JDesigner is a tool that allows users to visually design biochemical networks. In addition JDesigner will output standard scripts such as SBML and Jarnac script. JDesigner is also SBW compliant.
  • Jmol Tutorial Authoring Template (JTAT)
    Overview of available authoring tools for online macromolecular structure tutorials that utilize Jmol, and the home of one particular authoring template, JTAT.
  • JProfileGrid
    Site hosting v2.0 of JProfileGrid software for analyzing large multiple sequence alignments. A ProfileGrid matrix contains positional amino acid counts color-shaded according to the frequency of the characters in the alignment.
  • JProtAlign
    A java program for protein structure alignment and visualization.

  • - K -
  • KaKs_Calculator
  • Kaushik\'s Bioinfo. & Genomic (empty)
  • Kegg2Brenda (empty)
  • kgtests: Population expansion signatures
  • Kochanczyk Metaproject
    [This project serves as a placeholder that meets all the projects (present and future) developed by Marek Kocha?czyk in one place.]

  • - L -
  • La perception des couleurs par l\'oeil
    A science research project at the french school in brussels, created for the TPE projects in the french system. Deals with the perception of colors by the human eye. All information will be available to the public, but only in French.
  • Laboratory of Molecular Genetics, Hospital Motol, Prag
  • Language benchmark
  • Lapdog
  • LECB 2DgelDataSets database
    The LECB 2-D PAGE gel images database is for public use. It contains data sets from 4 types of experiments with 338 gif images with annotation and landmark data (various formats). It could be used for comparison with user data or software development.
  • Lectures in molecular biology (empty)
  • Leukemia genes database
    A database of leukemia genes
  • LHDFound Expert Support Group
  • Ligand Database (listed)
    Beta version of Ligand Database.
  • LindingLab
  • LINK{1,2,+} library (empty)
    << Not released any file yet >> An improvement of GOR-family algorithms for protein secondary structure prediction (LINK1, LINK2 and LINK+ methods). Based on GORx library.
  • Local Cell Metrics
  • LOLIPOG: LOg-LIkelihood for the Pattern Of Gaps in MSA
    This project aims to develop programs to calculate and use the log-likelihood for the pattern of gaps (LOLIPOG) in a multiple sequence alignment (MSA). Currently, only a Perl package, FA_LOLIPOG_P, is available at FTP repository.
  • Lung Cancer Gene Database
    LuGenD is developed to help the Biological and Medical Sciences community to easily access all information on the genes that are involved in Lung Cancer.

  • - M -
  • M.A.M.B.O (empty)
  • Mac5: Phylogenetic reconstruct (empty)
  • MACFAST BI & CB Group
  • Macroshack: Biolibrary of GUI macros
    The purpose of this project is two-fold. First of all, we would like to provide the average researcher with top-notch bioinformatics support. Second, we aim to provide a forum for bioinformaticians to distribute their work in a readily available form
  • MaHCO: An Ontology of the MHC
  • Malaria Drug Targets
  • MAMED: Pipeline for mapping-based analysis of metagenomic data
  • mappingapi: an api for the alignment of RDF models
  • massXpert (empty)
  • MatePred: SVM based prediction tool for MATE proteins
  • Matrix (empty)
  • Mattree: Phylogenetic analysis
    Phylogenetic analysis tools for distance matrix based clustering and comparison of trees.
  • Mavric: Phylogenetics toolkit
    Mavric is both a library of phylogeny manipulation routines and a graphical interface for phylogenetic tree visualization and editing.
  • Maximum contig size probabilities and metagenomics
  • MBAB bioinformatic group (empty)
  • MBAB Lab: miRFinder
    Bioinformatics tools and lab admistrations tools developed by Tinghua H. at MBAB lab.
  • MBEToolbox: Matlab toolbox for molecular evolution
  • MBI-Score: A multi-body interaction pose-scoring function
  • MBRC (empty)
    * Knowledge and Technology Infrastructure for Marine Biological Resource Center(s)MBRC(s): Focusing on integration of presently separate knowledge bodies and technology platforms for monitoring , inventoring and managing biodiversity and bioprospecting.
  • MCL-Dict (empty)
  • McSNP Base calling
    The software is to handle the base calling of the melting curve SNP genotyping technique. It aims to faciltate the practical use of this genotyping technology for clinical genetic tests.
  • MDAW (listed)
    Microbial Diagnsotic Array Workstation (MDAW) is a webserver designed for manging, sharing and analysing diagnostic array data. This is a free resource which can be accessed at
  • MedlineR
    We describe an open source library written in the R programming language for Medline literature data mining.
  • MeltSim: DNA melting simulator
    DNA melting simulator based on the algorithms of Poland, Scheraga, Fixman and Friere. Developed by Blake et al since 1980. More recent porting work done by Bizzaro.
  • Meta-analyses of indirect and mixed treatment comparisons
  • MetaBase CodeBase
    This project is for developing the software tools used to create and maintain MetaBase, the database of biological databases. The use of Perl MediaWiki API is demonstrated.
  • MetaBasis
    MetaBasis: A web based database (Basis) containing metadata (Meta) on software tools and databases in the field of Bioinformatics. Work done by: Vassilis Atlamazoglou PhD, Trias Thireou PhD, Yannis Hamodrakas MSc and George Spyrou PhD
  • Metabolic Reaction Analysis
  • MetaboSim: Metabolic pathway simulation
    In Contrast to low-level Petri Nets (Place/Transition nets), Coloured Petri nets (CPN) belong to the high level nets. The idea of CPN is to overcome some limitations of low level Petri nets by adding of higher programming languages.
  • MetaQTL
    MetaQTL is Java package for the meta-analysis of QTL mapping experiments.
  • MetaQuant
    MetaQuant is a software for the automatic and accurate quantification of GC/MS based metabolome data.
  • MFold Interface
    Develop a GUI interface using Perl/Tk to interact with Dr. Michael Zuker's web-based MFold. Will take in a sequence, GI, or accession number, obtain the sequence from GenBank, obtain folding parameters and results list, and then download results.
  • MICheckout: easy access to bioscience reporting guidelines
  • Microarray Cel File Summarizer
    Micro cs is a Tool for Managing Affymetrix Binary Files through a Java Based Graphical User Interface. Micro-CS is available as standalone tool or as a plugin for the TM4 platform allowing the management of binary affymetrix file within the TM4.
  • Microarray R US
    Featuring a user-friendly graphic interface, Microarray Я US is an R-based program that seamlessly integrates functions from over a dozen or so most-widely used Bioconductor packages to offer researchers a streamlined workflow to perform routine microarr
  • Microcirculation and hemorheology in critical illness
    Human microcirculation is critically affected by many disease states. Some of the changes can be visualized by side-stream dark field (SDF) imaging technology. Few reliable tools exists to analyze image data created by SDF imaging. Purpose of the gr
  • MicroRNA and Pathway Integrated Analyzer
  • microRNA Augmented Pathways (mirAP)
  • microRNA Recognition (empty)
  • Microsatellite Suite (empty)
  • MITS Bioinformatics: Misc. (empty)
  • MobBioTools: for hand-held devices
    Bioinformatics software has progressed a great deal from c++ code running on unix systems to user-friendly GUI based workbenches and visual tools. MobBioTools is a logical step forward towards bringing essential bioinformatics functionality to your mobile
  • Molecular visualization & structural bioinformatics
  • Molecular Visualization EMail List
    EMail list only: none of the Public Area resources are used.
  • Molekel
    Multiplatform Molecular Visualization Program
  • MolSlide Support
    ProteinExplorer.Org (PE) makes slides of rotatable macromolecular structure views (MolSlides.Org). (PE) works on-line or off-line (from a downloaded copy) except for saving MolSlides. This project will facilitate saving MolSlides in more situations
  • MolTalk: Biostructure library for Obj-C
    Development of a library and tools for object-oriented programming in Objective-C for macromolecular structure analysis. A Smalltalk-like interpreted scripting language gives access to all objects.
  • Motif Frequency Analyizer
  • MSAReveal
  • Msatfinder
    Msatfinder is a simple Perl script that detects perfect microsatellite repeats (1-6 bp) in nucleic acid or protein sequences. Longer motif lengths can be detected if desired, and a variety of output files suitable for further processing are generated.
  • mtRNA-seq
  • MuGeN: Multi-Genome Navigator
    MuGeN is a package for interactively exploring multiple annotated genomes simultaneously, possibly mixed with computational analysis results. Map information can be loaded from various sources, and resulting images can be exported in different formats.
  • Multi-threaded Java BLAST client (empty)
    A multi-threaded standalone (no web interface needed) Java BLAST client. It can run BLAST similarity searches based on input sequence(s) or the Request IDs given out by NCBI's QBLAST in both batch and multi-threaded modes.
  • Mutagenesis Primer Generator
    Simple Windows GUI program to generate mutagenesis primer by inputting sequence, amino acid number, and letter of amino acid you want to mutate to. Also customize scoring scheme to make the primer fit your own need.
  • Mutation Maker
  • (empty)
    The goal of this project is to develop a web-based user-friendly bioinformatics workstation where scientists can store and analyze their DNA/Protein sequences. A major goal is to have "plug-in" ability for developers and scientists to add tools/features t

  • - N -
  • NanoString-Splice
  • NCBI2RDF: a tool to enable RDF-complian access to the NCBI d
  • NeedleHaystack
  • NeoBio: Algorithms in Java
    NeoBio is a library of bioinformatics algorithms implemented in Java. The current version consists mainly of (pairwise) sequence alignment algorithms such as the classical dynamic programming methods of Needleman & Wunsch and Smith & Waterman.
  • Netsplitter: Interactive Metabolic Subnets
    Netsplitter is a Mathematica software application to split biochemical networks into functional subnetworks. The download includes a user guide giving details, and a full description is available in BMC SysBio 2011 5: 25
  • NETTAB Workshops (listed)
    A series of workshops on advanced network tools for bioinformatics. Next edition NETTAB 2017 "Methods, tools & platforms for Personalized Medicine in the Big Data Era", Oct 16-18, Palermo, Sicily, Italy.
  • Neural Network Roguelike Engine
  • neuroMiner: Your gateway to comparative microarray analysis
    neuroMiner aims to house and integrate the results of published microarray experiments from selected neurodegenerative diseases (Alzheimer's disease, Huntington's disease, Multiple sclerosis, and Down syndrom).
  • News & Commentary
  • No3CoGP: Non-Conserved and Conserved Coexpressed Gene Pairs
  • Not Another Protein Interaction Database
  • Numerical Taxonomy: (empty)
  • Nutrigenomics Knowledge Base: Resource for Nutrition Science

  • - O -
  • OligoCounter: a genome analyser
    OligoCounter is a Java command line program which counts overrepresented 8-14bp oligonucleotides in DNA sequences. Simple text output is produced which can be visualised with a suite of associated Java applications, for example JCircleGraph or OligoViz.
  • OligoFaktory Standalone Edition
  • Ontologizer Computational Biology(empty)
  • Open Access India
  • Open Personalized Health (empty)
  • Open source software from the Laboratory of Systems Biology
  • OpenBNS: Naming service (listed)
    The Biomolecule Naming Service (BNS) is an LDAP directory of gene and protein information derived from NCBI's LocusLink database. The purpose of BNS is to quickly and easily convert between different name and identifier schemes.
  • OpenClinica (empty)
  • OpenLIMS: Lab information system
    An open source laboratory information system designed aimed at small labs who want security and data exchange in an open system based on public protocols.
  • OpenMicrobio: The OpenSource Synthetic Biology Platform
  • OpenMMS Users Group (empty)
    OpenMMS (although defunct) has many nice features. DBLoader? This group needs to be renamed! The main component of this group is currently just the mailing list.
  • OpenNotebook: Data management
    The goal of the OpenNotebook project is to create a modular framework for a client side cross-platform application to assist the end user of a web-based scientific resource in storing and maintaining returned data.
  • Operon Group at UFSM
    The Operon Group is constituded of undergraduate students of Biology, Biochemistry, Informatics and Public Relations courses at the Federal University of Santa Maria ( More information in
  • Optimus CME (empty)
    Researching practical computational methods to solve the Chemical Master Equation (CME) using distrubuted/parallel algorithms executed on small PC clusters (10 processors).
  • Orlania Project (empty)
  • Otto Warburg java Library of structural bioinformatics (OWL)
    A java library for protein structure analysis
  • OX2 Bioinformatics (empty)
    Cybernetic & Logitronic concepts to formulate variables (input/output) computations for the oxygen element throughout its electrochemical behavior, inside and outside the body.

  • - P -
  • p53 Data Warehouse
  • PAAAPA: Polymorphic Amino Acid (empty)
  • PaMSA: A parallel algorithm for global protein MSA
    PaMSA is a parallel algorithm for global multiple sequence alignment of proteins
  • Pancreatic cancer genes database
    A database of pancreatic cancer genes
  • parallelsearch (empty)
  • ParaProbe (empty)
    Is a parallel distributed framework for the design of oligonucleotides suitable for microarrays.
  • PartiGene: EST analysis
    PartiGene is an integrated sequence analysis suite consisting of a set of scripts; trace2dbEST,, prot4EST, annot8r and wwwPartiGene which process and organise EST data within a genomic context and facilitate large scale analysis.
  • Partition Decoupling (empty)
  • Pastel
  • Pathogenicity Island Prediction Software
    PIPS is a software developed intending to identify Putative Pathogenicity Islands in pathogenic bacteria integrating the prediction of several algorithms. Later Versions of PIPS are planned that will turn the application faster and more accurate.
  • Patristic
    Patristic is a Java program that uses as input different tree files and computes their patristic distances. Patristic allows saving and editing in different ways those distances. Patristic provides different graphic views of the results.
  • PCalc: Primer concentration calculator
    PCalc is a software designed to help molecular biologists in routine procedures of concentrations calculus in PCR, like calculus of primer concentration, calculus of annealing temperature (DNA/DNA and DNA/PNA), MW primer calculation and mass units convers
  • pcb2png: PCB/PNG format converter
    pcb2png is a small utility that converts phosphoimager pcb/img files to png format
  • PDBHighlight: A Rasmol script DB
    PDBH aims to develop a searchable database of rasmol scripts, designed to visually integrate data in the PDB with data from other sources. Curently we maintain a set of scripts which DEFINE, color and annotate PDB entries with their SCOP domain definition
  • PDBWiki
    PDBWiki provides community features for users of the Protein Data Bank. It serves as a bugtracker, discussion forum and community annotation site for structures in the PDB.
  • PeakAnalyzer
  • PeCoP: Persistently Conserved Positions
    User submits a protein sequence, and retrieves the positions which are well-conserved through several PSI-BLAST iterations. Conservation is parameterized by use of aa alphabet, use of priors, and voting scheme.
  • Peptide confirmation algorithm (empty)
  • PerlKOB: Knowledge-based objects in Perl
    Extension of perl OO system influenced by Frames / ontology research
  • PES: Project For Endangered Species
    PES: Project For Endangered Species web based server side scripting backend with mysql or pgsql database. cataloging species and searching, adding functions.
  • pfp_pp: Function Prediction using Phylogenetic Profiles
  • PGA (empty)
  • PGEToolbox: Matlab toolbox for population genetics
  • Pharmaceutical Proteome (empty)
  • PhenoMan
  • Phenotyper
    Phenotyper is a system for collecting phenotyping data especially for plant breeding and science using handhelds for data input and web tools both for creating schemes for the user interface and managing result data.
  • PhilBioinformaticsOrg (empty)
    The Network for Integrative Multidisciplinary Bioinformatics Utilization Strategies (NIMBUS)-The Philippines' Bioinformatics Initiative
  • Phoenix
    Phoenix is a C++ parser for EMBL-Bank flat files.
  • PHP Labware
    PHP Labware develops PHP software like the LabStoRe LIMS and OrderSys ordering/purchase systems for day-to-day usage by research groups/laboratories
  • phpDAS: PHP modules for DAS (empty)
  • PHPLabDB
  • phpMesEchantillons: Samples management
    a web interface to manage biological samples (species, samples, DNA sequences, PCRs)
  • phpPhyloTree: Draw phylogenetic trees
    phpPhylotree is a web application that is able to draw phylogenetic trees. it produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.
  • PhyloFlow
  • Phylogenomics by Metabolomics and Proteomics
  • PHYLOGEOrec: Phylogeography Reconstruction for QGIS (empty)
  • PhyloMINE: A Phylogenomic (empty)
  • Pie Lab (empty)
  • PinkThing (empty)
  • Pipeline Environment
  • Plant Pathogen Microarray Meta-Database
  • PM-BLAST (empty)
  • POEM
  • Poly: Quantitative analysis of SSRs
    Poly is a program for the quantitative analysis of simple sequence repeats (SSRs) in DNA.
  • polyxmass: The massists\' program
    polyxmass is a software suite for (bio)polymer mass spectrometry that is Free Software developed on GNU/Linux. It allows the definition of polymer chemistries and the simulation/analysis of mass spectrometric data obtained on (bio)polymers.
  • Pool Models for Tracer Data (empty)
  • Populations: Gene frequencies
    Population genetic software: individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions.
    PORTRAIT (acronym for Prediction of transcriptomic ncRNA by ab initio methods) is an algorithm for identifying non-coding RNAs on a transcriptome context.
  • PQcalc: An online calculator for science learners
  • Preclinical data management (empty)
  • PREP: Perl RegExps for Pubmed
    PREP is a Perl script designed to allow the usage of regexps within searches of Pubmed. PREP allows for the easy retrieval of Pubmed records that contain terms that can be more easy matched by a textual pattern than a traditional keyword query.
  • primer3 Interest Group (empty)
  • PrimerMatch: PCR Primer Alignment Tools
    Tools for aligning PCR primers or similar short DNA sequences against genomic sequence. Many options for constraining acceptable alignments and input/output formats. Automatically optimizes the sequence search stategy for search parameters.
  • PrimerPy
    PrimerPy is a free GUI tool for optimal QPCR primer design, using "Primer3" as a backend engine. The design's been validated by laboratory experiences; applicable to conventional PCR too.
  • PrimerX: Mutagenic PCR primer design
    A web-based program that automates design of mutagenic PCR primers for site-directed mutagenesis.
  • PriMux: k-mer based library for genomic investigations
  • Prometheus: Analysis of chip-chip and expression microarrays
  • PROMPT (listed)
    PROMPT is a platform independent system for retrieval, analysis, mapping and comparison of protein sets. It allows easy mapping of different types of sequence identifiers, automatical data retrieval and integration, a multitude of analysis and comparison
  • ProPlus: Protein analysis system (empty)
  • Proscurator: Prostate oncogene (empty)
    catalogs the available known prostate oncogenes.
  • Protein Data Bank (PDB) File Editor
    User friendly PDB (Protein Data Bank) file editor with graphic user interface Tool for protein crystallographers to expedite selective edit / data extraction / analysis of their PDB files
  • Protein Functions Group (empty)
  • ProteinCharge (empty)
  • Proteopedia-list
    EMail list for the community of users of Proteopedia.Org. Proteopedia is hosted at the Weizmann Institute of Science (Israel).
  • PRP8 Protein Information Resource
  • Pubmed RSS --> Daily RNA interference article feed
    Daily delivery of RNA interference related news, articles and more.
  • PyAnnHyb
  • PyMsXML: Translate MS data to XML
    PyMsXML is a python script for converting vendor specific mass spectrometry data files from their proprietary binary format, to either of the emerging XML file formats for mass spectra: mzXML or mzData.

  • - Q -
  • Q Assembler
  • qcscreen
  • qPyCR
    A Python-based tool for accurate analysis of qPCR data using global fitting

  • - R -
  • Rapid Miner
  • Rare Variant Generalized Disequilibrium Test
  • Rare Variant Transmission Disequilibrium Test
  • RDFBuilder: RDF-based access to ArrayExpress
    RDFBuilder is a Java library that allows performing SPARQL queries to ArrayExpress microarray repositories. This library can be freely downloaded and used in other software projects.
  • RDFScape: Semantic Web and data analysis
  • REannotate
    Automated molecular palaeontology of repetitive DNA elements. Input: RepeatMasker annotation. Outputs: 1) Defragmentation of elements. 2) Inference of nesting structure. 3) Estimates of the ages of LTR-elements. 4) Multiply aligned element sequences.
  • Reconfigurable Bioinformatics (empty)
  • Reference Gene Database
  • REGULATOR: a database of metazoan transcription factors
    REGULATOR: a database of metazoan transcription factors and maternal factors for developmental studies
  • Regulatory Network Program (empty)
  • RESCUT (empty)
  • Reveal: Active-site recognition
  • Risk Allele Distribution Visualizer
  • RNA Web Services
  • Rosette Plotter Tool (empty)
  • Roskilde University Centre MMR (empty)
  • RPM repository for R and its packages
    An RPM repository for CRAN and BioConductor (including the R-forge repository).

  • - S -
  • S.aureus microarray meta-database
  • S2S: Sequence to Structure
  • sastra Bioinformatics (listed)
    A bioinformatics data-updater. This small PHP code would retrieve the current release files from the premier databases, parse it, and then list only the salient features all in one single go.
  • Satellite Prediction (empty)
  • SBEToolbox: Matlab toolbox for systems biology & evolution
  • SBML Inverse Eigenvalue Analyzer
  • Scriptome: Biological Data Manipulation
    The Scriptome is a set of tools and protocols that helps biologists format, merge, and filter files. While designed for non-programmers, it can also help beginners learn Perl if they choose, and serve as a "cookbook" for experienced programmers.
  • SEARCHPATTOOL: Pattern mining
    SEARCHPATTOOL is a program for analyzing DNA sequences in order to discover patterns or motifs for binding sites. It is based on exhaustive algorithm and is dedicated to prokaryotic species or genes with small promoter regions.
  • Secretion System Prediction Tool
  • seKs: Sequence editing KDE suite (empty)
    seKs will be an easy to use sequence editor, running in the KDE3 environment. It will provide a nice GUI to edit, analyze and anotate DNA, RNA and protein sequences. Status: heavy development, nothing for the public yet Dependencies: QT3, boost
  • SeqCut: DNA sequence cutting tools
  • SeqDoC: Chromatogram comparisons
    SeqDoC (Sequence Difference of Chromatograms) aligns and performs a subtractive comparison of two ABI DNA sequence chromoatograms. The subtracted profile is processed to highlight differences characteristic of single base changes.
  • SEQLinkage
  • seqPlotter (empty)
  • Sequence Extractor
    Accepts a DNA sequence and a set of primer sequences and returns a textual figure showing the annealing positions of the primers, restriction cut sites, and protein translations. Nested JavaScript code makes the figure interactive.
  • Sequence Manipulation Suite 1
    The Sequence Manipulation Suite 1 is a collection of web-based programs for analyzing and formatting DNA and protein sequences.
  • Sequence Manipulation Suite 2
    The Sequence Manipulation Suite 2 is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, and for teaching purposes.
  • Sequence Property Calculator (empty)
  • Sequence search mailing list
    The mailing list to ask all your SEQUENCE SEARCHING questions!
  • Sequences Studio: Biolibrary for Java
    Sequence Studio main package provides classes and interfaces for various kinds of sequence alignment
  • SEQUEROME: Sequence profiling tool
    SEQUEROME is a web-based Sequence profiling tool that provides a unique feature of completely profiling a BLAST report within a single browser interface by providing simplified access to web-distributed resources for protein and nucleic acid analysis.
  • SeWeR
    SeWeR is an very popular integrated, customizable, platform-independent web interface to bioinformatics services available over WWW.
  • Sight: Web robot generator
    Sight, a java-based package that provides a user-friendly interface to create and connect agents for automatic genomic data mining for individual purposes. No programming skills are required, but very strong support for programmers is implemented.
  • SigNetView: Signalling Network Viewer & Analyser
  • SimPed: simulate pedigree genotype
  • Single Channel Microarray Normalization
  • Site Editors
    This is the administration group.
  • SiteFind Development Group
    SiteFind is a molecular biology tool that enables a scientist performing site-directed mutagenesis to simultaneously introduce a restriction site as a maker for successful mutagenesis.
  • SLIMS group (empty)
  • SLRI Bioinformatics Toolkit (listed)
    The Samuel Lunenfeld Research Institute (SLRI) Bioinformatics Toolkit is a mainly C-based cross-platform toolkit for dealing with biological information, especially protein structure/function. Visit our project home page for more information.
  • Smith-Waterman on GreenTea
    A Smith Waterman sequence alignment algorithm implemented to run on GreenTea P2P decentralized distributed network computing platform
  • SNA: Stoichiometric Network Analysis
    SNA is a Mathematica toolbox for stoichiometric network analysis. Among other things, it supports flux balance analysis and the enumeration of the elementary vectors of the flux and the conversion cone.
  • SnapShotPriming (empty)
    Design primers for Snapshot to do allele specific analysis
  • SNBA: Synergistic Network Builder and Analyser
  • SNEASER: an easy SNP filter pipeline
    SNEASER is a perl based pipeline to detect potential exonic mutations in next generation sequencing data by filtering out all known variants.
  • SNP Tools for MS-Excel
  • SNPsel
    SNPsel generates allelic sequences by combining a single sequence with its SNPs, used as input for TFBS prediction programs (MULAN, MAPPER, MatInspector) to find TFBS affected by SNPs on both (allelic) sequences.
  • SolanGENE: Software listing (listed)
  • SPADE users and developers
  • Spatkin: Rule-based modeling on the plasma membrane
  • Specifying Cytokine network (empty)
    A n illustrative example for the current situation in immunological research is the case of cytokine networks. Cytokines are small protein or glycoprotein messenger molecules that convey information from one cell to another. Various aspects of the immune
  • SPIDER: Scoring protein-protein complexes
  • Sqwiki: The SQL enabled Wiki (empty)
    The idea is to combine a 'wiki' system with SQL queries, allowing data driven pages to be constructed by the user. The most important aspects are results formatting and parameter passing between data driven pages. The major hurdle is security.
  • SSAKE: Short sequence assembly
    The Short Sequence Assembly by K-mer search and 3' read Extension is a genomics application for aggressively assembling millions of short (25-36bp) nucleotide sequences.
  • Statistical power analysis for exome association studies
  • Statistics Online Computational Resource (SOCR)
  • StemNet
    The StemNet project aims at designing and constructing a knowledge management system for the field of stem cell biology. Its goal will be to increase security and the quality of clinical treatment based on enhanced, web-based information supply.
  • StoreHere: Sequence data storage (empty)
  • Strainer
    Strainer is a multi-platform visualization tool for metagenomics data. It allows the user to easily browse the variation present in assembled shotgun sequence data from non-clonal samples.
  • STRAP: 3-D sequence alignment
    The computer program STRAP supports the analysis of hundreds of proteins and integrates amino acid sequence, secondary structure, 3D-structure and genomic- and mRNA- sequence and residue annotation.
  • STRAPutils: CL tools derived from STRAP alignment program
  • Structural Classification Of Ligands
    The objective of the SCOL project is to produce a global hierarchical clustering of all the available small molecules and protein ligands using measures of structural and chemical 'similarity' between molecules.
  • StructureKit (empty)
  • sujatha madras veterinary college
  • Surface Plasmon Resonance Analysis Integration
    OSPRAI is the Open-source SPR Analysis and Integration software. This project develops interactive command-line tools for accessing, viewing, analyzing, and saving sensorgram from various surface plasmon resonance instruments including microarray imagers
  • SurpResi: Active site from central distances of atoms
  • SurpResidue: Active site from central distances of atoms
  • SVD fuzzy K
    The project is to develop an efficient and useful clustering algorithm. The project currently includes computer code written in Matlab for performing singular value decomposition followed by fuzzy K-means clustering on adjacency matrices.
  • Swift (empty)
  • Systems Bio Lab (empty)

  • - T -
  • t-CWT: Multivariate Assessment of Event-Related Potentials
    Free and open source software implementation of t-CWT for MATLAB and GNU Octave. t-CWT is a method for multivariate assessment of event-related potentials (ERP) based on the continuous wavelet transform (CWT) and Student's t-test.
  • tagsnper (empty)
  • TaxInspector
    A Java taxonomy browser GUI designed to run as a plugin or standalone. Currently works with the NCBI taxonomy.
  • Tb Drug Target Database
    This Database will give details of Drugs and the targets involved in the treatment of TB.
  • Telemedicine Research Laboratory (empty)
    Telemedicine Research Laboratory began its activities in the year 2000 at Bangalore, India. Some of the key objectives was to use technology for humanitarian purposes and synergise with international organisations like ITU and ISO.
  • TeXMed: A BibTeX interface for PubMed
    TeXMed is a simple web-interface to query NCBI PubMed to export references in bitex format.
  • Text2Knowledge: Text mining tools
    Text2Knowledge is aiming to provide text mining tools for medical texts. It utilizes natural language processing techniques to extract patterns for specific domains...
  • TfReg: DNA and RNA mesoscopic models
    TfReg implements the Peyrard-Bishop model for DNA and RNA duplexes. You can use it to calculate melting temperatures by entering the strength of the hydrogen bond or to obtain sequence-dependent opening profiles.
  • Thai Bioinformatics World Wide
  • The Coral Transcriptomics Network (CTN)
  • The Distributome Project
  • The Pogo Group
  • The Web Engine: A simple grid system
    Imagine that every web server was a generic CGI calculator, and you could compile code to 'run on the web'...
  • Three-Dimensional Superimposer (empty)
  • Tools to manipulate structural data in PDB format
  • TPE des 1res S du LFB 2001-2002
    Un "catalogue" de tous les TPE crs par les lves de 1re S au Lyce Francais de Belgique, pendant l'anne scolaire 2001-2002.
  • TraceGD
    Trace Genetic Disease detects position and type of the mutation when disease causing protein sequences are given as input and displays original and mutated amino acid sequences with the probable diseases.
  • TraceViewer (listed)
    TraceViewer provides several functionalities needed by any biologist who wants to efficiently analyse his/her trace data.
  • Transcription regulation analysis tools
  • Transcription regulation in plants
  • TreeQTL
  • TROLL: Tandem repeat locator (listed)
    The Tandem Repeat Occurrence Locator is a light weight SSR finder based on a slight modification of the Aho-Corasick algorithm.

  • - U -
  • UAN catmap webservice
  • UC Davis Medicago Bioinfo (empty)
  • UCD Bioinformatics & Comp. Biomedicine
  • UniDPlot: UniDimensional Plot
  • UniGene Dynamic Local Storage Tool
    The Dynamic Local Storage Tool is a simple PHP/Apache/MySQL application that downloads and maintains local databases containing relational UniGene keys for selected species.

  • - V -
  • VeaR: The structural highlighter
    [structural proteomics | JavaWebStart, OpenGL] Applies methods of defining conformational subspace for early-stage protein folding/structural similarity estimation by means of geometrical parameters of the polypeptide chain (see Bioinformatics papers)
  • Virtual Supermarket
  • VirusBanker
  • Visual Bioinformatics Tools (empty)
  • Visualization of Protein Ligand Graphs
  • VLinux: Bioinformatics Workbench
    VLinux Bioinformatics workbench is a Linux distribution for Bioinformatics. It is easy to use, no installation required, CD-based distribution. It includes a variety of sequence and structure analysis packages.It is an Open source product released under G
  • Volcanic earthworms: mitochondrial genome

  • - W -
  • W-curve: Genomic string visualization
    The W-curve is a numerical mapping, pattern recognition algorithm that shows significant potential for achieving visual consensus for the class of long repetitive sequences found in long genomic strings.
  • Wasabi (empty)
    The name (without the a?s) stands for ?Web Services for Bioinformatics?. Wasabi is both an initiative to refactor popular informatics utilities as Web services and a piping infrastructure enabling those services to be linked to solve complex problems.
  • WAX: Wide Area XML system
    WAX is general framework for tying together XML based applications on the web using RDF. Some code in CVS.
  • WinBLAST
    WinBLAST is a Windows graphical front-end for NCBI BLAST. It is written completely in C#, utilizing Microsoft?s latest .NET framework. WinBLAST will run on any Windows machine that supports Microsoft .NET framework. WinBLAST has an intuitive user inter

  • - X -
  • X-CHEM Multiplatform Molecule (empty)
  • Xenonucleic Acid Computing Group
  • xml4mat: XML/MATLAB format converter
    Simple, declarative, bijective inter-conversion between MATLAB structured variables and XML strings. A specialized markup language, MbML, was defined to support string representation of any MATLAB variable: any XML --> MbML <--> MATLAB

  • - Y -
  • Yapp
    YAPP Eukaryotic Core Promoter Predictor. Searches for core promoter elements within a sequence of Eukaryotic DNA, and for putative synergistic combinations of these elements, such as an Initiator (INR) motif at -2 in combination with a DPE motif at +28.
  • Yeast snoRNA Database
  • Yet Another Metagenomic Annotation Prog.
    Yet Another Microbial/Metagenomic Annotation Pipeline/Program is a Perl application created for the NERC Microbial Metagenomics programme. It is designed to be a user-friendly way for Bio-Linux users to run a selection of first-pass annotation tools upon
  • Yinteraction
    Yinteraction is a software for predicting genetic protein-protein interactions and pathways in bakery yeast, Saccharomyces cerevisiae. It uses two databases derived of the BioGrid and the SGD databases.
  • YNGS
    YNGS assembles pair-end fastq data by starting from a seed and elongates the string loop by loop. Matching fastq fragments can be counted for each position and can be displayed for each loop.
  • Your Lab Data: LIMS + ELN (listed)
    Your Lab Data is a free web-based LIMS (Laboratory Information Management System), aimed at a typical small molecular biology laboratory. It allows lab group members to have their own private forum, events (training or meetings), ELN and a LIMS area.
  • Yucleosome
    The software displays a 3D model of DNA-Nucleosome interactions of experimental validated Nucleosome positions of the bakery yeast Saccharomyces cerevisiae. It displays the nucleosome core particle H3,H4,H2A,H2B and the 146 bp long DNA fragment.

  • - Z -
  • zEST: Gene discovery by EST clusters
    The goal of this project is to discover new genes or splice variants from bioinformatic analysis on EST (Expressed Sequence Tag) hoping the interest of biologist for "wet" analysis on the produced data.
  • Zonal Phylogeny Software (empty)

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