[Next-Generation Sequencing Book]
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  • 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.
  • ABI.pm: Chromatogram file
  • AbifTake (empty)
  • ABIParser.py
    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 'ace.pl' 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 http://www.pdb.org 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 http://bioinformatics.org/arrayalizer/ 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 www.asidb.com. 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)

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  • 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

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  • 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)

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  • 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.

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  • 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

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  • 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.

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