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ABCC Genome Annotation Project (empty) (C, Perl, PHP, Unix Shell, Java)    
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. (Python) 
ABI.pm: Chromatogram file (empty) (Perl) 
AbifTake (empty) (C++)
ABIParser.py - A python module for parsing ABI trace file (and hopefully ABI gel file too in the not-so-distant future). (Python)
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 (Perl)
ALiBio: Biolibrary for C++ - A C++ library of efficient algorithms for bioinformatics (C, C++, Perl)
Alkahest: High-throughput (empty) - Alkahest is an initiative to produce free open source software systems for high-throughput DNA sequence data management and analysis. (Perl, PHP)
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. (Java)
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. (Pascal/Delphi/Kylix)
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. (Other Language)
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. (Unix Shell)
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 (Other Language, Perl, PHP)
AntPred (empty) (C++, Perl)
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. (Other Language, Pascal/Delphi/Kylix)
Asap: A framework for promoter analysis (C, Python)
Assemble: a tool to construct and study RNA architectures (Java)
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. (Other Language, C++, PHP, Python)
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 (C++, Visual Basic)
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). (Perl, Unix Shell)
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 (Unix Shell, Java)
BIC CHOP (empty) (Perl, PHP)
BIC-INDORE (listed) (C, Perl, Visual Basic)
BicAT Plus: Biclustering method comparisons (Java)
Bifx Free Software Builds (empty) (C, C++, Unix Shell, TCL, Lisp)
Bio-Linux: A Linux OS distribution - Bio-Linux is a bioinformatics-centred distrubution based on Debian GNU/Linux. Currently at version 4, it provides standard and cutting edge bioinformatics tools. It is freely distributed via the NERC Environmental Bioinformatics Centre (NEBC), Oxford, UK (Other Language)
BIO-NIX: A Linux OS distribution (empty) (Unix Shell)
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. (Other Language)
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 (Other Language, C, C++, Java, Visual Basic, Lisp)
BioBrew: Package repository - BioBrew is a collection of open-source applications for life scientists and an in-house project at Bioinformatics.Org. (Other Language)
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. (Other Language)
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. (Other Language)
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 (C++, Python)
BioCocoa: Biolibrary for Obj-C - Open source, Objective-C framework for parsing and writing sequence file formats (Other Language)
BioECMA (empty) (Other Language)
Biogress: PostgreSQL for (empty) (Other Language)
Bioinformatics analysis at UNICZ.IT (C++, PHP, Java)
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. (Perl, Python, Unix Shell)
Bioinformatics database search (empty) (C, Perl, PHP, Java)
Bioinformatics Object-Oriented Modules - BOOM, the Bioinformatics Object Oriented Modules, is a collection of reusable classes for efficient object-oriented bioinformatics modeling and application development; it has been used in several gene prediction programs including TIGRscan and TWAIN. (C++)
Bioinformatics System Dynamics (empty) - This is a unique project that tries to make an informatic simulated system from a genetic /physiology well-known system. (Other Language, C, C++, Pascal/Delphi/Kylix)
Bioinformatics.Org - The Bioinformatics Organization, Inc. serves the scientific and educational needs of bioinformatic practitioners and the general public. (PHP, Python)
BioJafa (empty) (C, Python, Unix Shell)
BioLet: Wavelet analysis tools (empty) - Bioinformatics tools for performing wavelet analysis on DNA sequences (Other Language)
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. (Other Language)
Biometrical Methods (empty) (C, C++)
bioNMF: NMF in Biology (Pascal/Delphi/Kylix)
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.) (PHP)
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. (Java)
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. A typical use is to store and query sequence base ranges in a biological database. (C)
biosql on rails (empty) (Other Language)
BioSuite (empty) (Other Language, C, C++, Java)
BioSVG (Perl)
BioVM: Bioinformatics Virtual (empty) (Other Language)
BIRCH: Comprehensive bioinfo. system - BIRCH is comprehensive bioinformatics system, running on the Unix system. BIRCH consists of programs and databases for molecular biology that are useable either through a graphic interface or the Unix command line. The design of BIRCH lends itself to flex (Python, Unix Shell, Java)
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. (Perl)
blast2ps: Graphical overview of output - Fast and easy to use script producing a graphical overview of blast results. (Perl)
BLASTometer: Monitor BLAST jobs (Other Language)
Blaxter Lab (empty) (Perl)
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. (Perl)
BNA: Biological Network Analysis (C, C++, Perl)
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 (Perl)
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) (Other Language, Java)
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++)
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. (C, C++, Perl)
CBESW: Sequence Alignment on the PS3 (Other Language, C)
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 (C, C++, Perl)
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. (C++)
CGView (Java)
Chinook: P2P system using JXTA (listed) (Unix Shell, Java)
Chromhome: Comparative genomics DB - Chromhome (http://www.chromhome.org) is a database of comparative genomics showing maps of chromosome homologies across species. (Perl, Java)
CiteMan (PHP)
Clusterfunc: Clustering of functional categories (C++)
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. (Perl)
Coffee Mug: Hypertension genomics - WE strive to provide simple solutions for everyday life in a molbio lab (C, C++, Perl, Python, Unix Shell, Visual Basic)
COMBOSA3D: Molecule coloring - A web-based program for comparing sequence conservation patterns to three-dimensional structures. (Other Language)
Comparitive Genome Browser (empty) (Perl)
CRAIG (empty) (C++, Perl)
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. (C, Unix Shell)
Cyntenator: Progressive gene order alignments - Cyntenator is a software for identification of conserved syntenic blocks between multiple genomes. (C++, Unix Shell)
DBBP: BioPython tools (empty) (C, C++, Perl, Python, Unix Shell)
dChip: Gene Expression and SNP Genotyping (C, C++)
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. (Perl, Java)
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. (Python)
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. (C, C++, Python)
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 (Other Language, C++, Java)
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. (Perl, Java)
Distributed Computing Power Proj (empty) (Other Language)
DNACGR: D/RNA pattern visualization - Program to visualise patterns in DNA and RNA by using Chaos Game Representation (C)
DNALinux: Bioinformatics Virtual Machine - A Xubuntu Linux based virtual machine Bioinformatics environment. (Other Language)
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. (C++, Perl, Unix Shell, Java)
Ebbie: Small RNA analysis and storage (Perl, Unix Shell)
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 (Other Language, PHP, Java)
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. (Perl)
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. (C, C++)
ESPSim - ESPSim is an open source JAVA application designed to compute the similarity of protein electrostatic potential maps. (Java)
Excel2SVM (Python)
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. (Java)
eyeLIMS (PHP, Java)
FASIMU: Constrained optimization of metabolic networks (Unix Shell)
File Format Converter Tool (empty) (Perl, PHP, Java)
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. (Other Language)
fishpathogens.net (empty) (Perl, PHP)
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 (PHP)
Format Conversion Tool (empty) (Perl, PHP)
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. (C++, Visual Basic)
FreeMOL Compilation - FreeMOL is a compilation of free and open source programs forming a framework for computational chemistry, informatics, structural biology and graphics. (C, Python)
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. (C, C++)
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 Bioinformatics.Org is discontinued. Please proceed to the home page at http://www.g-language.org/.) (Other Language, Perl)  
GAMESS Dispersion Module (C++)
GB-CARTool (empty) (Perl, Java, Visual Basic)
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). (Other Language)
GEMS (empty) (Other Language)
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. (Other Language, C)
GenBank Creator (empty) (Perl, PHP)
Gene Cluster with Literature Profiles (Visual Basic)
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. (Java)
Gene Ontology Browsing Utility (empty) (Java)
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. (Java)
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. (Other Language)
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 (Other Language, Java, Visual Basic)
Genes Interactions Simulation (listed) - Gints aims at the simulation of regulation networks. (Java)
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. (Python, Java)
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. (C)
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 (PHP, Java)
GeneZilla - GeneZilla (formerly TIGRscan) is a state-of-the-art GHMM-based eukaryotic gene finder. It is faster and uses significantly less memory than GENSCAN, with comparable accuracy. (C++)
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. (C++, Perl, Java)
Genome Assembly Script (empty) (Perl)
Genome Display Tool (Java)
Genomic Re-Annotation Tool (empty) (Other Language)
Genopolis database codebase - This this the codebase for the Genopolis Gene Expression database (http://www.genopolis.it). It is presented here for futher puplic development or as a resource for similar projects. (PHP, Java)
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. (C, Unix Shell)
Genquire: Genome browsing and annotation - Browsing and Annotation of complete or incomplete genomes. Live GUI-manipiulation of the underlying database (with write access). (Perl)
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. (Perl, Unix Shell)
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. (Other Language, C++)
GORx library (empty) - << Not released any file yet >> GOR-family algorithms for protein secondary structure prediction. (Other Language, C, PHP, Python, Unix Shell, TCL, Lisp)
GPBlast: Search for homologous/paralogous protein sequences (Perl)
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. (Python)
Harwell Informatics (empty) - under development (Perl, PHP, Unix Shell, Java)
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. (Other Language)
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. (Other Language, C, PHP, Python, Unix Shell, TCL, Lisp)
HydrophobicityPlot - The program calculates a hydrophobicity plot. Several sets of parameters can be used. (under construction) (Java)
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. (PHP)
Ishmael: BioMOBY browser - Ishmael is a standalone browser for the BioMOBY Biological Web Services system. Source is in CVS. (Perl)
IsoScan: Isochore boundary (empty) - IsoScan uses a 4-state Hidden Markov Model to predict isochores (regions of homogeneous G+C content) in genomic DNA. (C++, Perl)
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, ... (Other Language)
JaMBW: Molecular biology workbench - Java based Molecular Biologist's Workbench (Other Language, Java)
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)
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 (Other Language, Perl, Unix Shell, Java)
Java interface to the M-CL algorithm (C, C++, Unix Shell, Java)
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. (Other Language, Java)
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. (Java)
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. (Pascal/Delphi/Kylix)
Kegg2Brenda (empty) (Java)
kgtests: Population expansion signatures (Visual Basic)
Kochanczyk Metaproject - [This project serves as a placeholder that meets all the projects (present and future) developed by Marek KochaÅ?czyk in one place.] (C, Perl, Unix Shell, Java)
Lapdog (Perl)
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. (Other Language, C, PHP, Python, Unix Shell, TCL, Lisp)
Local Cell Metrics (C++, Python, Unix Shell)
Mac5: Phylogenetic reconstruct (empty) (C++)
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 (Other Language)
massXpert (empty) (C++)
Mattree: Phylogenetic analysis - Phylogenetic analysis tools for distance matrix based clustering and comparison of trees. (C++)
Mavric: Phylogenetics toolkit - Mavric is both a library of phylogeny manipulation routines and a graphical interface for phylogenetic tree visualization and editing. (Python)
MBAB Lab: miRFinder - Bioinformatics tools and lab admistrations tools developed by Tinghua H. at MBAB lab. (C++, Perl, Python)
MBEToolbox: Matlab toolbox for molecular evolution (Other Language)
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 http://www.arraydb.org (Other Language, PHP, Java)
MedlineR - We describe an open source library written in the R programming language for Medline literature data mining. (Other Language)
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. (Pascal/Delphi/Kylix)
MetaBase CodeBase - This project is for developing the software tools used to create and maintain <b><a href="http://MetaDatabase.Org">MetaBase</a></b>, the database of biological databases. The use of Perl MediaWiki API is demonstrated. (Other Language, Perl, PHP, Unix Shell)
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. (Other Language)
MetaQTL - MetaQTL is Java package for the meta-analysis of QTL mapping experiments. (Java)
MetaQuant - MetaQuant is a software for the automatic and accurate quantification of GC/MS based metabolome data. (Java)
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. (Other Language, Perl)
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. (C, C++, PHP, Java)
microRNA Recognition (empty) (C, C++, Perl, PHP, Python, Unix Shell, Java)
MITS Bioinformatics: Misc. (empty) (C, C++, Perl, Python, Unix Shell, Java, Visual Basic)
MLPERCEP (Other Language, C)
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 (Java)
Molekel - Multiplatform Molecular Visualization Program (C++)
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 (Other Language)
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. (Other Language, C)
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. (Perl)
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. (Perl)
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. (Java)
muscorian (empty) (Other Language, C, Perl, Python, Java, Pascal/Delphi/Kylix)
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. (Visual Basic)
MyBioinformatics.com (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 (Perl, PHP, Python)
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. (Java)
Neural Network Roguelike Engine (Java)
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). (Other Language, PHP)
Not Another Protein Interaction Database (Other Language)
Numerical Taxonomy: (empty) (Visual Basic)
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. (Java)
OligoFaktory Standalone Edition (Other Language)
Open Personalized Health (empty) (PHP)
OpenClinica (empty) (PHP, Java)
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. (Perl, Java)
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. (Java)
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). (C++, Java)
PAAAPA: Polymorphic Amino Acid (empty) (Other Language)
parallelsearch (empty) (C++)
ParaProbe (empty) - Is a parallel distributed framework for the design of oligonucleotides suitable for microarrays. (Perl, Unix Shell)
PartiGene: EST analysis - PartiGene is an integrated sequence analysis suite consisting of a set of scripts; trace2dbEST, PartiGene.pl, prot4EST, annot8r and wwwPartiGene which process and organise EST data within a genomic context and facilitate large scale analysis. (Perl, PHP)
Pastel (Perl)
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. (Java)
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 (Other Language, Visual Basic)
pcb2png: PCB/PNG format converter - pcb2png is a small utility that converts phosphoimager pcb/img files to png format (C, C++)
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 (Perl, PHP)
Peptide confirmation algorithm (empty) (C, C++)
PerlKOB: Knowledge-based objects in Perl - Extension of perl OO system influenced by Frames / ontology research (Perl)
PGA (empty) (C++, Perl)
PGEToolbox: Matlab toolbox for population genetics (Other Language)
Phoenix - Phoenix is a C++ parser for EMBL-Bank flat files. (C++)
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 (PHP)
phpDAS: PHP modules for DAS (empty) (PHP)
phpLabDB (listed) - Built around independent modules that interact with each other, phpLabDB manages a variety of day-to-day useful laboratory information. It is also a high powered and highly customisable open-source laboratory database project. (Other Language, PHP)
phpMesEchantillons: Samples management - a web interface to manage biological samples (species, samples, DNA sequences, PCRs) (PHP)
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. (PHP)
PhyloMINE: A Phylogenomic (empty) (Perl, PHP)
Plant Pathogen Microarray Meta-Database (PHP, Java)
PM-BLAST (empty) (Other Language, C++, Perl)
Poly: Quantitative analysis of SSRs - Poly is a program for the quantitative analysis of simple sequence repeats (SSRs) in DNA. (Python)
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. (C)
Populations: Gene frequencies (listed) - Population genetic software: individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions. (C++)
PORTRAIT - PORTRAIT (acronym for Prediction of transcriptomic ncRNA by ab initio methods) is an algorithm for identifying non-coding RNAs on a transcriptome context. (C, Perl, Python)
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. (Perl)
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. (C++)
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. (Python)
PrimerX: Mutagenic PCR primer design - A web-based program that automates design of mutagenic PCR primers for site-directed mutagenesis. (Perl)
Prometheus: Analysis of chip-chip and expression microarrays (Other Language, Perl)
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 (Java)
ProPlus: Protein analysis system (empty) (Java)
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 (Java)
ProteinCharge (empty) (C, Perl, PHP)
PyAnnHyb (Python)
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. (Python)
Q Assembler (Other Language)
RDFScape: Semantic Web and data analysis (Java)
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. (Perl)
Reconfigurable Bioinformatics (empty) (Other Language)
RESCUT (empty) (Perl)
Reveal: Active-site recognition (Java)
Rosette Plotter Tool (empty) (Perl)
S2S: Sequence to Structure (Java)
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. (PHP)
Satellite Prediction (empty) (Other Language)
SBEToolbox: Matlab toolbox for systems biology & evolution (Other Language, C)
SBML Inverse Eigenvalue Analyzer (Other Language)
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. (Perl)
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. (C++)
Secretion System Prediction Tool (C, C++, Perl, Unix Shell)
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 (C++)
SeqCut: DNA sequence cutting tools (Perl, PHP, Unix Shell, Java)
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. (Perl)
seqPlotter (empty) (Perl, Java)
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. (Other Language, Perl)
Sequence Manipulation Suite 1 - The Sequence Manipulation Suite 1 is a collection of web-based programs for analyzing and formatting DNA and protein sequences. (Other Language)
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. (Other Language)
Sequence Property Calculator (empty) (C, Visual Basic)
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. (Java)
SeWeR - SeWeR is an very popular integrated, customizable, platform-independent web interface to bioinformatics services available over WWW. (Other Language)
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. (Java)
SigNetView: Signalling Network Viewer & Analyser (Java)
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. (Java)
SLIMS group (empty) (Java)
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. (C)
Smith-Waterman on GreenTea - A Smith Waterman sequence alignment algorithm implemented to run on GreenTea P2P decentralized distributed network computing platform (Java)
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. (Other Language, C)
SnapShotPriming (empty) - Design primers for Snapshot to do allele specific analysis (Perl, PHP)
SNP Tools for MS-Excel (Other Language)
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. (Other Language)
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 (C++, Java)
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. (Other Language, Perl, PHP, Unix Shell, Java)
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. (Perl, Python)
StoreHere: Sequence data storage (empty) (Other Language)
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. (Java)
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. (C, C++, Unix Shell, Java)
StructureKit (empty) (Perl)
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. (Other Language)
SWeBLAST (Perl)
Swift (empty) (C, Perl, Java)
tagsnper (empty) (Perl)
TaxInspector - A Java taxonomy browser GUI designed to run as a plugin or standalone. Currently works with the NCBI taxonomy. (Java)
TeXMed: A BibTeX interface for PubMed - TeXMed is a simple web-interface to query NCBI PubMed to export references in bitex format. (Perl)
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... (C, C++, Perl, PHP, Unix Shell, Java, Lisp)
The Pogo Group (C++, Visual Basic)
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'... (Other Language)
Three-Dimensional Superimposer (empty) (C++)
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. (C, C++, Perl)
UC Davis Medicago Bioinfo (empty) (Other Language)
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. (PHP)
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) (Java)
VirusBanker (Java)
Visual Bioinformatics Tools (empty) (C, C++)
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 (Other Language)
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. (C++)
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. (Other Language, C++, Perl, PHP, Java)
WAX: Wide Area XML system - WAX is general framework for tying together XML based applications on the web using RDF. Some code in CVS. (Perl, Python, Java)
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 (Other Language, C, C++)
X-CHEM Multiplatform Molecule (empty) (Other Language, C)
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 (Other Language)
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 (Perl)
Zonal Phylogeny Software (empty) (Perl)
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