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Softwares Used in Biotechnology and Molecular Biology Studies


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DNA Analysis Software (Downloads)

The Java based Molecular Biologist's Workbench.

a tool for working with and managing nucleotide sequences in multiple formats.

a software for chromatogram files created by sequencers.

DNA Sequence Polymorphism, is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data.

a compact, easy to use DNA analysis program, ideal for small-scale sequencing projects.

a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation.

(Artemis Comparison Tool) is a DNA sequence comparison viewer based on Artemis.

Genetic Data Analysis software

the industry standard software for DNA sequence analysis.

The ultimate thermodynamic modelling spreadsheet for Excel

be useful in the detection of duplication events in genomes, tracking the "footprints" of evolution, as well as displaying the genetic maps and other aspects of comparative genetics.

allows to visualize genescan files (.fsa format from ABI PRISM sequencers) and to view the exact peak size.

a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank, EMBL, or DDBJ sequence databases.

an integrated DNA/Protein analysis tool package for molecular biology/biotech researchers.

allows graphic manipulation of DNA sequences and sophisticated plasmid drawing options.

a DNA sequence comparison tool and graphical user interface (GUI) viewer implemented in Perl/Tk.

a genome annotation viewer and editor

a tool for SNP Search and downloading with local management

SSRHunter 1.3 Simple Sequence Repeat Search tool

Internet Contig Explorer

DNA analysis program

DNA sequence analysis program

The free Sequence Scanner Software enables you to view, edit, print and export sequence data generated using the Applied Biosystems Genetic Analyzers.

a program for sequence assembly, contig editing, and mutation detection, available for Windows and Mac OS X.

an application for Win95/Win98/Win NT for analysis of nucleotide sequences.

tool for alignment, SNP identification, and PHRAP evaluation.

A graphic tool to visualize DNA sequences.

software for DNA cloning, sequence analysis and visualisation,

Stand alone Chromatogram Editor with Mutation Detection

Tool shows the proportions between nucleotides in a DNA sequence

Tool will list all chromatogram files (SCF, ABI, AB1, AB) in the current folder.

Nucleotide Sequence Analyzer

This program is designated to manage microsatellite data

e-Workbench for "databasing", comparative genome analysis.

Integrated Genome Browser

software for automated gene annotation and functional classification

DNA sequence editor and analysis package

Circular and linear interactive genome visualisation.

Java application used to display SNPs in a genetic context.

NCBI Genome Workbench.

A software tool for discovering transcription factor binding motifs.

    

Software tool designed to find repeats, from 3 bp to 64 bp length, in circular genomes

Auxiliary DNA Software.

Software for DNA sequence assembly, DNA sequence analysis etc.

A sequence analysis tool.

DNA Sequence Contig Assembler Software

An open source, platform independent tool for genomic data

RNA Analysis Software (Download)

an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows

a Windows program for the prediction and analysis of RNA secondary structure.

a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules.

a tool for drawing RNA secondary structures in molecular biology.

program for inferring RNA secondary structure using the comparative method.

a Java applet for viewing RNA secondary structures and linking to multiple computational backends.

programs for the prediction and comparison of RNA secondary structures.

a Java based suite of tools for the creation, annotation and display of RNA secondary structure diagrams.

a new XML web service and web application program for visualizing RNA secondary structures with pseudoknots.

Researchers use the OligoEngine platform to design sequences and purchase oligos,

RNA/DNA folding predictions including pseudoknots and entangled helices

a tool for folding RNA secondary structures, including the class of simple recursive pseudoknots.

abstraction maps structures to a tree-like domain of shapes

an algorithm for finding genomic targets for microRNAs

program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.

a simple software tools that enables to display all secondary structures of a family of RNA molecules.

A utility for collecting statistics from aligned and structurally annotated RNA sequences.

software for RNA analysis

A Design and Visualization Tool for RNA Secondary Structure.

An extension of DNA Baser, specialized in processing rRNA sequences.

highly effective, target specific siRNA online design site.

a program for improved detection of transfer RNA genes in genomic sequence.

3D Molecular Modeling Software (Download)

an excellent and free molecular viewer.

a molecular visualization software adapted from the program RasMol

combines state of the art molecular graphics with a full range of Windows desktop integration tools.

a fully Windows integrated, 3D molecular renderer.

reads PDB files or alignment files directly from the database

view and display 3D ICM graphical slides and animations interactively inside Microsoft PowerPoint and web browsers

is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc.

a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service.

interrogate the 3-dimensional structure of biological macromolecules as found in the Protein Data Bank (PDB) using query and display tools

Desktop Molecular Modeller ( DTMM ) is a simple-to-use molecular modelling program .

a tool for the visualization and analysis of molecular structures and their chemical properties.

creates three-dimensional, photo-realistic images using a rendering technique called ray-tracing.

a custom unofficial version of POV-Ray with a lot of additional features.

molecular modelling program.

graphics file converter that reads Brookhaven Protein Data Bank format files and produces a ready-to-render input file for the Persistence of Vision ray tracer (POV-Ray).

a chemical visualization and illustration program with a new graphic interface.

a MS-Windows version of the current release of ORTEP-III (1.0.3).

a versatile crystallographic tool implementing a large variety of standard geometrical calculations

a 3D vector display program which shows "kinemage" graphics.

prepares molecular kinemages (input files for Mage & KiNG) from PDB-format coordinate files

an interactive system for three-dimensional vector graphics.

an application that provides a user friendly interface allowing to analyze several proteins at the same time

an editor for molecules that allows the input of chemical structures in a very comfortable way.

Java3D Molecular Visualisation System

a molecular viewer, animator, analyzer, and MOPAC reaction path

converter.

an integrated high quality system for building and modelling molecules (Mopac and Iconc are included) and the system drives PC GAMESS and Tinker.

will work in stand alone mode or under Oscail and will use Tinker Files if Tinker has been installed

molecular modeling software

molecular modeling and visualization program

full-featured molecular modeling and visualization tool designed for Windows.

Convert two-dimensional structures from ACD/ChemSketch into their three-dimensional

molecular visualization system on an OPEN-SOURCE foundation.

a program for viewing molecular structures and animating molecular trajectories.

free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules

a highly extensible, interactive molecular graphics program.

a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry.

It has been specially designed to focus solely on the ?, ^ and ? angles.

A single, integrated application for your desktop * Hand optimized 3D for complex molecules

view chemical structures from within popular Web browsers,

is available for free and contains all the functions you need to explore a macromolecular structure interactively.

a free program for protein structure model-building, visualization, validation and analysis ...

a versatile package for the analysis, rebuilding, and visualization of three-dimensional nucleic acid structures, based on a standard reference frame

A molecular modeling, graphics, and drug design program

a program for the macromolecular structure visualization on the Windows platform

a free program for visualizing and manipulating molecules.

a suite of freeware and shareware tools for automating work of rendering and animating molecules

3D-Graphics program for Molecular Modeling and Visualization of Quantum Chemical Calculations

It's the evolution of the well known VEGA OpenGL package and includes several new features and enhancements making your research jobs very easy.

a GTK based program for the display and manipulation of isolated molecules and periodic systems

an extensible object oriented class library, written in C++ for representing the 3-dimensional structure of biological macromolecules.

open source (GPL), interactive, high quality molecular visualization system

programs for molecular modeling

BALLView 1.3

standalone molecular modeling and visualization application

Software to prepare and present structure annotations containing formatted text, graphics, sequence data, and interactive molecular views

Molecular visualization tool.

User friendly PDB (Protein Data Bank) file editor

A Molecular Modelling suite for drug design.

Protein Data Bank Viewer.

An advanced molecular editor.

An open source workbench for chemo- and bioinformatics.

A molecular graphics program.

Molecular Viewer Applet.

Free Organic Chemistry Analysis and Visualisation Tool

A software tool that allows to derive 3D pharmacophores from structural data of macromolecule/ligand complexes.

A suite of automated docking tools

3D Chemical Visualization and Decision Support.

Virtual Screening software for Computational Drug Discovery.

Add Proteins and DNA in 3D stereoscopic viewer

Software for molecular visualisation.

software package that integrates modeling, crystallography and NMR spectroscopy.

Freeware product for presentation of molecules.

A Public Domain Molecular Modeling Software.

Protein Analysis Software (Download)

ANalyse THE PROTeins software.

Protein Sequence Analysis And Modelling

a graphical Viewer and editor for Helical Membrane Protein Topologies

Membrane Protein Explorer

a tool for visualization and manipulation of complex interaction networks.

for visualizing large-scale protein interaction networks.

General Protein/Mass Analysis for Windows

Systematic Tailored Orf-data Retrieval & Management

Protein Interactions VisualizatiOn Tool

A versatile tool for the analysis of aminoacid sequences.

a Java-application for constructing multiple protein sequence alignments from regions of high similarity.

An advanced workbench for protein analysis.

a SmartTag and Add-In solution for the Microsoft Office applications.

The first computational system for predicting protein submitochondria locations from its primary sequence.

The Protein Coverage Summarizer

Tools and software libraries for proteomics data analysis.

Hydrogen Bond Analysis Tool.

A tree viewer for hierarchical clusterings of proteins in the human Genome.

Biochemical Engineering

Bioreactor Design software

Fermentor Control Program

Program for Dynamic Simulation of Fed-Batch Penicillin Production

tool for process and product development engineers

PCR

Unique and innovative primer design studio

A comprehensive primer design tool to design

Oligo 6.71 Demo researchers in PCR and related technologies software

Software for pASK-IBA and pPR-IBA Vectors

tool to efficiently design hundreds of specific oligos

Beacon Designer 5.10 Demo helps design successful molecular beacon

Free! Primer Analysis Software

to facilitate the design of PCR primers

Electronic PCR (e-PCR) is computational procedure that is used to identify sequence tagged sites(STSs), within DNA sequences.

a free software for design PCR primers

a multi-user, multi-platform oligonucleotide cataloguing application

a free, open-source GUI application that designs primers for PCR.

software for seeking in a collection of primers

developed to rapidly screen previously selected PCR primers

a desktop tool to design primers for site directed mutagenesis kits.

Java Application for automatical primer design.

a PCR primer design tool that completely automates the primer design process.

Absolute estimation of initial concentrations of amplicon in a real-time RT-PCR process

Sequence Format Conversion

A powerful sketchpad to decorate your sequence.

Visual Sequence Editor

tool for the conversion of nucleic acid and amino acid sequence alignments

a free sequence file format conversion utility by GeneStudio, Inc.

a modern suite of molecular biology applications for the Windows platform built on our sequence format conversion engine, SeqVerter

a program for processing nucleotide sequences alignment made with FASTA and BLAST alignment tools.

creates the reverse complement of a DNA sequence

code for handling and manipulating biological sequences.

a fast and efficient compression algorithm for DNA sequences

Advanced Protein Sequence Converter

a conversion program for bioinformatics.

a command line program designed to extract the structure information (.pdb) from the xml structure files.

Sequence Manager And Converter .

a tool for converting DNA or protein data file to formats usable in major analytical software.

software tools for merging muti-files in a single file.

Tool will split a multi-FASTA file in multiple standard FASTA files.

Utility to convert the binary file format from an ABI PRISM TM 377 DNA Sequencer to an xml file

automatic ABI to FASTA Converter

a freeware that can convert GenBank (gb/gbk) file format to FASTA format.

A Batch DNA Sample Converter.

Phylogenetic Analysis

Phylogenetic Analysis Using Parsimony

Paup Windows Interface software

the PHYLogeny Inference Package

a simple program for displaying phylogenies

an experimental program for comparing gene and species trees.

NEXUS Data Editor) is a program to create and edit NEXUS format data files

an experimental program for comparing host and parasite trees

a freeware utilities package that works with the phylogenetic inference package Phylip

a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.

a Java tool for the visualization of annotated phylogenetic trees

a software package developed primarily for the construction and drawing of phylogenetic trees

program for analysing evolutionary trees

a tree drawing program able to draw any phylogenetic tree

Molecular Evolutionary Genetics Analysis

Selection on Amino Acid Properties

software for evolutionary biology

Analysis Library A Java library for molecular evolution and phylogenetics

a collection of command line programs written in Java to access some selected features in PAL

application for computing evolutionary networks from molecular sequence data.

a Java computer program to estimate gene genealogies including multifurcations and/or reticulations (i.e. networks).

a program for the calculation of the statistics and associated P-values for the nested clade analysis (NCA) developed by Templeton and collaborators.

Recombination detection program

a distance based phylogeny reconstruction algorithm.

an integrated environment for the manipulation and phylogenetic analysis

Tree and Reticulogram reconstruction

a computer package for PCs which estimates and tests gene diversities and differentiation statistics from codominant genetic markers

A tool for the construction of large phylogenetic trees based on profile distances

a new distance-based clustering method, triplet clustering algorithm

tests of differential diversification rates

Phylogenetic Visualization tool

computes phylogenetic trees from molecular sequences.

a software package for PHylogenetics And Sequence Evolution

Bayesian Analysis in Molecular Biology and Evolution

phylogenetic model averaging

a windows and linux interface for modeltest.

determining the optimal phylogenetic supertree

to conduct the Test For Serial Independence (TFSI) on continuously valued characters and the Runs Test on discretely valued characters (Abouheif 1999)

a java implementation of the evolutionary trace method

program for making phylogenetic trees starting from sequence data

implements some straight-forward birth-death models for simulating phylogenies

cross-platform program for Bayesian MCMC analysis of molecular sequences

Macroevolutionary Analysis & Simulation

Compare phylogenetic evolutionary trees interactively and automatically

display a phylogenetic tree in several different styles

a comprehensive phylogenetic tree visualization and manipulation software

a computer program that simulates the branching of an evolutionary tree

Genealogy Interval Explorer

Phylogenetics, Evolutionary Biology, and Bioinformatics in a moduLar Environment

a program for building and displaying phylogenetic trees

a drawing tool for creating phylogenetic trees.

a program for the Bayesian estimation of phylogeny,

software for generating evolutionary trees and networks ,

Phylogenetic Data Editor

software for Parsimony ratchet analyses with PAUP.

provides an easy and fast access to cophylogenetic analyses

An interactive viewer for large phylogenetic trees

A graphical editor for phylogenetic trees.

Primer design and sequence statistics for phylogenetic DNA data sets

A tool to aid in the classification & evolutionary relationships of protein sequences.

Dnamic graphics and annotations for phylogenetic or classification trees analyses .

An editor for large phylogenetic trees written in Java.

A graphycal software to perform phylogenetic analyses.

An application for comparing two trees using coupled interaction.

An application that allows to build, visualize and customize phylogenetic trees.

A graphical viewer of phylogenetic trees.

A program for qualitative analysis of sets of trees.

Plasmid Map

Virtual cloning laboratory.

Scientific software for the molecular biologist

visual, intuitive and integrated molecular cloning software

solution for fast and easy plasmid map drawing,restriction site mapping, and virtural cloning

tool for drawing publication and vector catalog quality maps

A Plasmid Editor

DNA plasmid drawing software

A plasmid drawing software.

a DNA mapping program for Mac OS

Circular Genome Viewer

A free, cross-platform PLAsmid MAnipulation program

Online Tools

automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input.

Online Plasmid map drawing

Draw plasmid map tool.

Free online plasmid draw/plotter program.

Image Analysis

a free image processing and analysis program

Java image processing program

An image processing package.

PC software package, developed for analysis of genetic fingerprints such as RFLP, RAPD and AFLP

Image analysis software for Gel Electrophoresis samples

the Windows version of Scion Image, which is in turn a version of the popular Macintosh program, NIH Image, written at the National Institutes of Health.

a viewer for Papyrus / DICOM images (the actual standard for viewing, storing acquiring, communicating radiological and non-radiological medical images).

visualize gels and related data obtained through the use of the full version of ImageMaster 2D Platinum or Melanie by colleagues. I

software range for the fast and accurate analysis of 1D gel images.

software to analyze a wide variety of material including polyacrylamide and agarose gels

digitizing software converts an image file showing a graph or map, into numbers.

for digitization of orthogonal graphs

for automatic processing of spectra and also any plots having strongly expressed local maxima (peaks).

A feature-filled, user friendly software product, provided free of charge to scientists

a program for digitizing graphs and plots.

application that makes it easy to acquire, measure, and analyze digital images

software replaces a digitizer tablet.

software for quantification of labeled bacteria by automated image analysis.

Display a grid over your image.

free open source software for analysis, processing and 3D rendering of multi dimensional microscopy images.

Program for making publication-quality 2D and 3D scientific graphs.

Cross-Platform Advanced Thin Layer and Gel Analysis Software.

1D gel electrophoresis analysis software .

Software for Tissue MicroArrays (TMA's).

Software for the analysis of DNA fingerprints.

A miniature utility for gel image analysis.

3D/4D/5D Image Visualization & Analysis System for Bioimages

3D software tool.

Sequence Alignment Analysis

genome & proteome research tools

Multiple Alignment Construction & Analysis Workbench

multiple alignment program for DNA or proteins.

Compares a protein sequence to another protein sequence or to a protein database, or a DNA sequence to another DNA sequence or a DNA library.

A Full Featured Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows.

The Basic Local Alignment Search Tool

a biological sequence editor and analysis program

a biological sequence alignment editor written for Windows 95/98/NT/2000/XP.

Data Analysis and Molecular Biology and Evolution software

a graphical multiple sequence alignment editor

a multiple alignment editor written entirely in java

Bioinformatics software

a revolutionary new Windows application for DNA and protein sequence analysis.

a freeware program, allows scientists to study and analyze biological molecules.

an innovative software tool that provides helpful gene analysis capabilities in an intuitive and easy-to-use interface.

program for sequence editing and population genetics (mol/evol) analysis.

The Sequence Manipulation Suite

A fully developed set of DNA sequence assembly (Gap4), editing and analysis tools

a dynamic, flexible open source platform for the integration of bioinformatics software tools and databases.

a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements)

Sequence analysis and data management software

an acronym, stands for SEquence analysis using WEb Resources.

a Windows graphical front-end for NCBI BLAST.

A Graphical Tool for Sequence Feature Visualization and Comparison

a Java front end to many useful bioinformatics tools

Blast local tools

local pairwise sequence alignment software

sequence analysis tools

tools for sequence analysis.

bioinformatics analyses workbench.

a multiple sequence alignment program.

a multiple sequence alignment program.

graphical program for visualizing local alignments between two sequences

Bioinformatics Algorithms in Java

Multiple Sequence Alignment Interactive Program

Genome Alignment Software

tool for viewing and manipulating the output from pairwise alignment programs

DNA local alignment tool

Molecular Structure Viewer and Colour INteractive Editor for Multiple Alignments

Bioinformatics Toolbox for analysis of biomedical data

a software for DNA and amino acid editing

multiple alignment software

Multiple alignment and editor software.

tools for basic and advanced analyses of nucleotide and protein sequences.

software to explore BLAST results graphically

highly flexible framework for designing biomolecular viewers.

a bioinformatics software tool for analyzing DNA and protein sequences.

statistical and evolutionary analysis of multiple sequence alignments

A visualization tool to simultaneously integrate and analyze multiple types of genomic data.

The European Molecular Biology Open Software Suite

A Python platform for structural bioinformatics.

genomics Workbench , a Java-based open-source platform for integrated genomics.

Structure and Sequence Alignment Software.

Integrated Bioinformatics Tools.

A tool for generating annotated multiple sequence alignments.

Bio-Chip

Process fluorescent images of microarrays

Perform a variety of types of cluster analysis and other types of processing on large microarray datasets.

Graphically browse results of clustering and other analyses from Cluster

provides high performance robotic control of microarrayer robots

software package for analysis and visualization of microarray data

Java-based data-mining facility for cDNA or oligonucleiotide microarray databases

programs for viewing and optimizing gene expression dendrograms

DNA-Chip Analyzer (dChip) (www.dchip.org) is a Windows software package for probe-level and high-level analysis of Affymetrix gene expression microarrays and SNP microarrays

Significance Analysis of Microarrays

visualization and statistical analysis of DNA microarray gene expression data

program for organizing, exploring, visualizing, and analyzing microarray data

DNA Macroarrays Analysis Program

expedient determination of the quality of multiple spotted DNA microarray experiments

enhanced version of Cluster

analytic tools for genomic data

Gene Map Annotator and Pathway Profiler

primary data entry, tracking, and reporting system.

multi-channel image analysis tool for microarray images

a normalization and filtering tool used to process the raw data output from Spotfinder

main data analysis and visualization tool for microarray

program for reordering and displaying expression array data.

Viewer for Microarray Data in the PCL or CDT format

EXpression Analyzer and DisplayER

a program that computes gene specific oligonucleotides that are free of secondary structure for genome-scale oligonucleotide microarray construction.

Bayesian Analysis of Gene Expression Levels (BAGEL): a program for the statistical analysis of spotted microarray data.

a computer program for the analysis of temporal gene expression data.

Gene Array Analyzer Software

a statistical analysis program to identify differentially expressed genes from microarray data

Statistical analysis is based on the single-factor ANalysis Of VAriance (ANOVA)

toolkit for analyzing tabular data within the framework of rough set theory.

tools for microarray

a program for microarray image quantification

a set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data

a program that compares heterologous microarray data sets, based on the number of common, differentially expressed genes.

Microarray Image Analysis Software ,

MicroArray Genome Imaging & Clustering Tool.

Add-In for Microsoft Excel, which is designed to handle the microarray data.

application for analysing array-experiments.

A workbench for visualization, analysis and storage of microarray data.

Microarray Probe Designer.

a software tool to extract gene expression modules from perturbational microarray data

Software for gene expression microarray data analysis.

Java application for microarray data analysis.

An Excel plug-in that performs sparse canonical correlation analysis.

Oligo Microarray Design and Analysis

An application for significance analysis of microarrays using a parallelized algorithm.

A Java program for analysis and visualization of Affymetrix GeneChip? data.

Education

the demonstration of Main Metabolic Pathways for PC

Linear Pathway Simulator

let them experiment with the simulation

The Molecular Basis of Medicine

Photosynthesis a tutorial program for photosynthesis

a self-training program based on PBL (Problem-Based- Learning Pathway) built to simulate a molecular biology laboratory.

Computer aided learning for quantitative genetics.

computer programs for the teaching and learning of genetics.

Cell Structure & Function education software.

Digital Frog software

Cell Tissue Body explorer.

Education software for BIO

Painlessly teach anyone he must-know details of how DNA works in 3D.

equence Alignment Teacher.

Animations and Graphics

icons for scientific programs.

Prescott, Harley, and Klein's Microbiology, 7/e

Robert J. Brooker, Biology, 1st Edition

biologically related images.

From Japanese RIKEN Center for Developmental Biology

Interesting Stuff

a player for Conway's game of life

Experience life and death in a window or as a screen saver!

an entertaining plant breeding game

to create impressive simulations of complex systems

screen saver offers individuals a tremendous amount of variety

a "screen saver" of images by Irving Geis

Screen saver demonstrating DNA chain termination caused by Acyclovir

converting DNA sequences into music.

Molecular Probes Screensaver

a distributed computing project

This 3D screensaver shows real 3D models of biological molecules in dynamics

Inside the Cell 3D screensaver will provide you with a unique opportunity to plunge into the very depths of the living organism

a game about SNP and side effort

Virtual Electron Microscope

Microbiology Screensaver

converts the text of a DNA or protein sequence to a MIDI file

program that simulates bacteria-like organisms

fills your screen with scrolling C/G/A/T

artificial life simulation

artificial life simulation

Screen Saver.

BRAINY SCREEN SAVER

the software simulates in a visual fashion the processes involved in the evolution of unicellular organisms at nature,

a Tcl/Tk application for turning DNA sequences into musical sequences

Gaming software.

Addictive puzzle game.

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