3D Molecule |
|
| RASMOL 2.7.5.2 |
an excellent and free molecular viewer. |
| RasTop 2.2 |
a molecular visualization software adapted from the program RasMol |
| DS Visualizer 3.1 |
combines state of the art molecular graphics with a full range of Windows desktop integration tools. |
| ICM-Browser 3.7 2b |
reads PDB files or alignment files directly from the database |
| ActiveICM 1.1.6 |
view and display 3D ICM graphical slides and animations interactively inside Microsoft PowerPoint and web browsers |
| VMD 1.9 |
is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. |
| CN3D 4.3 |
a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. |
| WPDB 2.2 |
interrogate the 3-dimensional structure of biological macromolecules as found in the Protein Data Bank (PDB) using query and display tools |
| DTMM 4.2 Demo |
Desktop Molecular Modeller ( DTMM ) is a simple-to-use molecular modelling program . |
| gopenmol 3.0 |
a tool for the visualization and analysis of molecular structures and their chemical properties. |
| POV-Ray 3.7b38 |
creates three-dimensional, photo-realistic images using a rendering technique called ray-tracing. |
| MegaPov 1.2.1 |
a custom unofficial version of POV-Ray with a lot of additional features. |
| Mol2Mol 5.6.3 Demo |
molecular modelling program. |
| MolPOV 2.0.8 |
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). |
| PovChem 2.1.1 |
a chemical visualization and illustration program with a new graphic interface. |
| Ortep-3 2.02 |
a MS-Windows version of the current release of ORTEP-III (1.0.3). |
|
PWT(PLATON for Windows Taskbar) 1.15 |
a versatile crystallographic tool implementing a large variety of standard geometrical calculations |
| Mage 6.44 |
a 3D vector display program which shows "kinemage" graphics. |
| Prekin 6.42 |
prepares molecular kinemages (input files for Mage & KiNG) from PDB-format coordinate files |
| KiNG 2.20 |
an interactive system for three-dimensional vector graphics. |
| Swiss-PdbViewer 4.04 |
an application that provides a user friendly interface allowing to analyze several proteins at the same time |
| StrukEd Demo |
an editor for molecules that allows the input of chemical structures in a very comfortable way. |
| JMVC 4 041122 |
Java3D Molecular Visualisation System |
| Re_View 1.0 |
a molecular viewer, animator, analyzer, and MOPAC reaction path
converter. |
| Oscail X 2011 |
an integrated high quality system for building and modelling molecules (Mopac and Iconc are included) and the system drives PC GAMESS and Tinker. |
| Moilin X 2011 |
will work in stand alone mode or under Oscail and will use Tinker Files if Tinker has been installed |
| Tinker 5.1 |
molecular modeling software |
| Biodesigner 0.75 |
molecular modeling and visualization program |
| MoluCAD 1.034 Demo |
full-featured molecular modeling and visualization tool designed for Windows. |
|
Protein Explorer 2.80 |
free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules |
| Chimera 1.5.3 |
a highly extensible, interactive molecular graphics program. |
| Jmol 12.2.7 |
a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. |
| Ramachandran Plot Explorer 1.0 |
It has been specially designed to focus solely on the ?, ^ and ? angles. |
| ProteinScope LE 1.0.5 |
A single, integrated application for your desktop * Hand optimized 3D for complex molecules |
| CHIME 2.6 SP8 |
view chemical structures from within popular Web browsers, |
| YASARA View 11.9.18 |
Free and contains all the functions you need to explore a macromolecular structure interactively. |
| NOC 3.01 |
a free program for protein structure model-building, visualization, validation and analysis ... |
| 3DNA 1.5 |
a versatile package for the analysis, rebuilding, and visualization of three-dimensional nucleic acid structures, based on a standard reference frame |
| ArgusLab 4.0.1 |
A molecular modeling, graphics, and drug design program |
| CueMol 2.0.1.172 |
a program for the macromolecular structure visualization on the Windows platform |
| SweetMollyGrace 1.3 |
a suite of freeware and shareware tools for automating work of rendering and animating molecules |
| Facio 15.1.1 |
3D-Graphics program for Molecular Modeling and Visualization of Quantum Chemical Calculations |
| VEGA ZZ 2.4.0 |
It's the evolution of the well known VEGA OpenGL package and includes several new features and enhancements making your research jobs very easy. |
| GDIS 0.90 |
a GTK based program for the display and manipulation of isolated molecules and periodic systems |
| PDBlib 2.2 |
an extensible object oriented class library, written in C++ for representing the 3-dimensional structure of biological macromolecules. |
| QuteMol 0.4.1 |
open source (GPL), interactive, high quality molecular visualization system |
| Ascalaph 1.7.12 |
programs for molecular modeling |
| BALLView 2.0-r1 |
standalone molecular modeling and visualization application |
| BioEditor 1.6.1 & BioViewer 1.5.7 |
Software to prepare and present structure annotations containing formatted text, graphics, sequence data, and interactive molecular views |
| ProteinShader beta 0.9.4 |
Molecular visualization tool. |
| PDB Editor 090203 |
User friendly PDB (Protein Data Bank) file editor |
| Zodiac 0.65 |
A Molecular Modelling suite for drug design. |
| mmPDBViewer 2009.3.20.4 |
Protein Data Bank Viewer. |
| Avogadro 1.0.3 |
An advanced molecular editor. |
| Bioclipse 2.4.0 |
An open source workbench for chemo- and bioinformatics. |
| Antheprot 3D 1.0.162 |
A molecular graphics program. |
| Chemis3D 2.89b |
Molecular Viewer Applet. |
| Chemitorium 4.0 |
Free Organic Chemistry Analysis and Visualisation Tool |
| LigandScout 3.03a |
A software tool that allows to derive 3D pharmacophores from structural data of macromolecule/ligand complexes. |
| AutoDock 4.2.3 |
A suite of automated docking tools |
| Benchware 3D Explorer 2.7 |
3D Chemical Visualization and Decision Support. |
| PyRx 0.8 |
Virtual Screening software for Computational Drug Discovery. |
| VisProt3DS 3.03 |
Add Proteins and DNA in 3D stereoscopic viewer |
| OpenAstexViewer 3.0 |
Software for molecular visualisation. |
COSMOS 5.0 PRO trial
COSMOS Viewer 3.0 |
software package that integrates modeling, crystallography and NMR spectroscopy.
Freeware product for presentation of molecules. |
| MOIL 12.0.3671 |
A Public Domain Molecular Modeling Software. |
| MMV 2.2.0 |
Molegro Molecular Viewer. |
| OpenMM 3.1.1 |
A library which provides tools for modern molecular modeling simulation. |
| OpenStructure 1.1.0 |
Open-source computational structural biology framework. |
| MMPRO 0.7 |
Molecule Visualization & Analysis Program |
DNA |
|
| jambw 1.1 |
the Java based Molecular Biologist's Workbench. |
| AnnHyb v.4.945 |
a tool for working with and managing nucleotide sequences in multiple formats. |
|
ChromasPro 2.33 |
a software for chromatogram files created by sequencers. |
|
DnaSP 5.10.01 |
DNA Sequence Polymorphism, is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. |
| DFW 2.51 trail |
a compact, easy to use DNA analysis program, ideal for small-scale sequencing projects |
| Artemis 13.2.0 |
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. |
| ACT 10.2.0 |
(Artemis Comparison Tool) is a DNA sequence comparison viewer based on Artemis. |
| GDA 1.1 |
Genetic Data Analysis software. |
| Sequencher 5.0 Demo |
the industry standard software for DNA sequence analysis. |
|
MeltCalc Lite
MeltCalc 2.06 Pro |
The ultimate thermodynamic modelling spreadsheet for Excel. |
| GenomePixelizer 2003.10.1 |
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. |
|
GenescanView1.2 4
GenescanView1.2 8 |
allows to visualize genescan files (.fsa format from ABI PRISM sequencers) and to view the exact peak size. |
| Sequin 11.75 |
a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank, EMBL, or DDBJ sequence databases. |
| Gene Construction Kit 3.5.1 Demo |
allows graphic manipulation of DNA sequences and sophisticated plasmid drawing options. |
| GenomeComp 1.3 |
a DNA sequence comparison tool and graphical user interface (GUI) viewer implemented in Perl/Tk. |
| Apollo 1.11.6 |
a genome annotation viewer and editor. |
| SNPHunter 1.75 |
a tool for SNP Search and downloading with local management. |
| SSRHunter 1.3 |
SSRHunter 1.3 Simple Sequence Repeat Search tool |
| iCE 3.5 |
Internet Contig Explorer. |
| MB6.84 |
DNA analysis program. |
| FinchTV 1.4 |
DNA sequence analysis program. |
| Sequence Scanner v1.0 |
The free Sequence Scanner Software enables you to view, edit, print and export sequence data generated using the Applied Biosystems Genetic Analyzers. |
| CodonCode Aligner 3.7.1.1 |
a program for sequence assembly, contig editing, and mutation detection, available for Windows and Mac OS X. |
| WinGene 2.31 |
an application for Win95/Win98/Win NT for analysis of nucleotide sequences. |
| BioLign 4.0.6 |
tool for alignment, SNP identification, and PHRAP evaluation. |
| SequenceViewer 1.0 |
A graphic tool to visualize DNA sequences. |
| SERIAL CLONER 2.1 |
software for DNA cloning, sequence analysis and visualisation, |
| Xplorer 2.4.2 |
Stand alone Chromatogram Editor with Mutation Detection. |
| DNA Counter v1.0.2 |
Tool shows the proportions between nucleotides in a DNA sequence. |
| Chromatogram Explorer 3.2 |
Tool will list all chromatogram files (SCF, ABI, AB1, AB) in the current folder. |
| NSA 3.3 |
Nucleotide Sequence Analyzer |
| YCDMA 3.1.1 |
This program is designated to manage microsatellite data |
| G-InforBIO V1.90 |
e-Workbench for "databasing", comparative genome analysis. |
| IGB 6.6 |
Integrated Genome Browser |
| goldMINER 2.0.27 |
software for automated gene annotation and functional classification |
| DNA Master 5.22.1 |
DNA sequence editor and analysis package |
| DNAPlotter 1.4 |
Circular and linear interactive genome visualisation. |
| AssociationViewer 2.0 |
Java application used to display SNPs in a genetic context. |
| gbench 2.4.0 |
NCBI Genome Workbench. |
| LocalMotif 1.0 |
A software tool for discovering transcription factor binding motifs. |
| RepeatAround 2.1 |
Software tool designed to find repeats, from 3 bp to 64 bp length, in circular genomes |
| DNAux 3.0 |
Auxiliary DNA Software. |
| DNA Baser 3.2.5 |
Software for DNA sequence assembly, DNA sequence analysis etc. |
| Seqool 3.1 |
A sequence analysis tool. |
| DNA Dragon 1.4.1 |
DNA Sequence Contig Assembler Software |
| CisGenome Browser 2.0 |
An open source, platform independent tool for genomic data |
| PriorsEditor 1.0.11 |
A general workbench for regulatory region analysis and transcription factor binding site discovery. |
| Savant 1.6.0 |
A desktop visualization tool for genomic data. |
| BiQ Analyzer 2.0 |
A software tool for DNA methylation analysis. |
| DNAmend 1.02A |
Cloning software. |
| BQGB 090528 |
Berkeley Quantitative Genome Browser. |
RNA |
|
| RNA draw |
an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows. |
|
RNAstructure 5.3 |
a Windows program for the prediction and analysis of RNA secondary structure. |
| RnaViz 2.0 |
a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. |
| loopDloop 2.07b |
a tool for drawing RNA secondary structures in molecular biology. |
| Circles 0.1.1 |
program for inferring RNA secondary structure using the comparative method. |
| SStructView 1.2 |
a Java applet for viewing RNA secondary structures and linking to multiple computational backends. |
| Vienna RNA Package 1.8.5 |
programs for the prediction and comparison of RNA secondary structures. |
| XRNA 1.2.0b |
a Java based suite of tools for the creation, annotation and display of RNA secondary structure diagrams. |
| PseudoViewer 3.0 |
a new XML web service and web application program for visualizing RNA secondary structures with pseudoknots. |
| OligoEngine 2.0 |
Researchers use the OligoEngine platform to design sequences and purchase oligos, |
| pknotsRG 1.3 |
a tool for folding RNA secondary structures, including the class of simple recursive pseudoknots. |
| RNAshapes 2.1.6 |
abstraction maps structures to a tree-like domain of shapes. |
| miRanda 201008 |
an algorithm for finding genomic targets for microRNAs. |
| RNAz 1.0 |
program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. |
| RnaFamily |
a simple software tools that enables to display all secondary structures of a family of RNA molecules. |
| RNApasta 1.01 |
A utility for collecting statistics from aligned and structurally annotated RNA sequences. |
| CLC RNA Workbench 4.5.2 |
software for RNA analysis. |
| RnaDv 1_0 |
A Design and Visualization Tool for RNA Secondary Structure. |
| RNA Baser2.77.2 |
An extension of DNA Baser, specialized in processing rRNA sequences. |
| Assemble 1.0.4 |
A graphical tool to construct and study RNA architectures |
| VARNA 3.7 |
Visualization Applet for RNA. |
| nocoRNAc 1.22.1 |
Software for non-coding RNA characterization. |
Protein |
|
| AnthePro 6.0 |
ANalyse THE PROTeins software. |
| PSAAM |
Protein Sequence Analysis And Modelling . |
| VHMPT |
a graphical Viewer and editor for Helical Membrane Protein Topologies. |
| MPEx 3.2 |
Membrane Protein Explorer . |
| Osprey 1.2.0 |
a tool for visualization and manipulation of complex interaction networks. |
| InterViewer 4.0 |
for visualizing large-scale protein interaction networks. |
| GPMAW 9.10 DEMO |
General Protein/Mass Analysis for Windows. |
| STORM 1.01 |
Systematic Tailored Orf-data Retrieval & Management. |
| PIVOT 2.0 |
Protein Interactions VisualizatiOn Tool. |
| WinPep3.01 |
A versatile tool for the analysis of aminoacid sequences. |
| PAT 0.9 |
a Java-application for constructing multiple protein sequence alignments from regions of high similarity. |
| CLC Protein Workbench 5.5.2 Demo |
An advanced workbench for protein analysis. |
| ProTag 1.4 |
a SmartTag and Add-In solution for the Microsoft Office applications. |
| SubMito 1.1 |
(the first computational system for predicting protein submitochondria locations from its primary sequence. |
| PCS 1.3.4053 |
The Protein Coverage Summarizer |
| ProteoWizard 2.0 |
Tools and software libraries for proteomics data analysis. |
| HBAT 1.1 |
Hydrogen Bond Analysis Tool. |
| ProteinVis 2.1.6 |
A tree viewer for hierarchical clusterings of proteins in the human Genome. |
| ProCope 1.2 |
Protein Complex Prediction and Evaluation Software. |
| PRIDE Converter 2.5.1 |
Converts mass spectrometry data formats into valid PRIDE XML |
Education |
|
| mmp.zip |
the demonstration of Main Metabolic Pathways for PC |
| linpath |
Linear Pathway Simulator |
| protlab 3.01 |
let them experiment with the simulation |
| molmed.zip |
The Molecular Basis of Medicine |
| Photo |
Photosynthesis a tutorial program for photosynthesis |
| Virtlab 2.0 |
a self-training program based on PBL (Problem-Based- Learning Pathway) built to simulate a molecular biology laboratory. |
| GENUP 5.5 |
Computer aided learning for quantitative genetics. |
| hands on genetics |
computer programs for the teaching and learning of genetics. |
| ScienceMatrix Demo |
Cell Structure & Function education software. |
| Digital Frog 2.5a |
Digital Frog software |
| CTB 2.0 |
Cell Tissue Body explorer. |
| Molecular Genetics 3.1 Demo |
Education software for BIO |
| OnScreen DNA |
Painlessly teach anyone he must-know details of how DNA works in 3D. |
| TOUR OF THE BASICS |
The animated tour of biology. |
| GeneExplorer 2.0.1 |
An interactive simulation of gene expression |
| Protein Investigator 3.0.2 |
A software to interactively explore protein structure and function. |
| Aipotu 1.3.2 |
Software to simulates the genetics, biochemistry etc. |
| VGLII 3.1.3 |
The Virtual Genetics Lab . |
| Ileum 3.0 |
Simulation of experiments on the isolated Guinea-pig Ileum |
Bio-Engineering |
|
| BRD 4.0 |
Bioreactor Design software |
| BioStat 4.4 |
Fermentor Control Program |
| PenSim v2.0 |
Program for Dynamic Simulation of Fed-Batch Penicillin Production |
| SuperPro Designer 8b06EF Demo |
tool for process and product development engineers |
PCR |
|
| NoePrimer 2.03 |
Unique and innovative primer design studio |
| Primer Premier 6.11 DEMO |
A comprehensive primer design tool to design |
| Oligo 7.55 Demo |
Oligo 6.71 Demo researchers in PCR and related technologies software |
| Primer D'Signer 1.1 |
Software for pASK-IBA and pPR-IBA Vectors |
| Array Designer 4.25 Demo |
tool to efficiently design hundreds of specific oligos |
| Beacon Designer 7.92 Demo |
Beacon Designer 5.10 Demo helps design successful molecular beacon |
| NetPrimer |
Free! Primer Analysis Software |
| TGGE-STAR |
to facilitate the design of PCR primers |
| e-PCR 2.3.9 |
Electronic PCR (e-PCR) is computational procedure that is used to identify sequence tagged sites(STSs), within DNA sequences. |
| FastPCR 6.2.59 |
a free software for design PCR primers |
| PerlPrimer v1.1.21 |
a free, open-source GUI application that designs primers for PCR. |
| AmplifX 1.5.4 |
software for seeking in a collection of primers |
| AutoDimer 1.0 |
developed to rapidly screen previously selected PCR primers |
| MutaPrimer 1.00 |
a desktop tool to design primers for site directed mutagenesis kits. |
| ORFprimer 1.6.4.1 |
Java Application for automatical primer design. |
| Primer Prim'er 5.6.0 |
a PCR primer design tool that completely automates the primer design process. |
| PCR Analyzer 1.02 |
Absolute estimation of initial concentrations of amplicon in a real-time RT-PCR process |
| Methyl Primer Express 1.0 |
Software to design high quality PCR primers for methylation mapping experiments. |
Conversion |
|
| SeqCorator 2.03 |
A powerful sketchpad to decorate your sequence. |
| vised11.exe |
Visual Sequence Editor |
| ForCon 1.0 |
tool for the conversion of nucleic acid and amino acid sequence alignments |
| SeqVerter 2.0.4.3 |
a free sequence file format conversion utility by GeneStudio, Inc. |
| GeneStudio Pro 2.1.2.4 |
a modern suite of molecular biology applications for the Windows platform built on our sequence format conversion engine, SeqVerter |
| FASTA/BLAST SCAN 2.1 |
a program for processing nucleotide sequences alignment made with FASTA and BLAST alignment tools. |
| RevComp 2.4 |
creates the reverse complement of a DNA sequence |
| BioCocoa 2.2.2 |
code for handling and manipulating biological sequences. |
| DNACompress |
a fast and efficient compression algorithm for DNA sequences |
| Readseq 2.1.30 |
a conversion program for bioinformatics. |
| XML2PDB |
a command line program designed to extract the structure information (.pdb) from the xml structure files. |
| DNAsmac 2.0.2.6 |
Sequence Manager And Converter . |
| DataConvert 1.0 |
a tool for converting DNA or protein data file to formats usable in major analytical software. |
Fasta2MultiFasta v08.10.31
multi-FASTA2FASTA 1.0 |
software tools for merging muti-files in a single file
Tool will split a multi-FASTA file in multiple standard FASTA files. |
| abi2xml 1.2 |
Utility to convert the binary file format from an ABI PRISM TM 377 DNA Sequencer to an xml file |
| ABI to FASTA converter 1.1.2 |
automatic ABI to FASTA Converter |
| GenBank to FASTA converter 08.11.12 |
a freeware that can convert GenBank (gb/gbk) file format to FASTA format. |
| Convertrix 1.0 |
A Batch DNA Sample Converter. |
Phylogenetic |
|
| WINIPAUP 1.0 |
Paup Windows Interface software. |
| Phylip 3.69 |
the PHYLogeny Inference Package |
| TreeView 1.6.6 |
a simple program for displaying phylogenies |
| GeneTree 1.3 |
an experimental program for comparing gene and species trees. |
| NDE 0.5.0 |
NEXUS Data Editor) is a program to create and edit NEXUS format data files |
| TreeMap 3.0b |
an experimental program for comparing host and parasite trees |
| Phyltools 1.32 |
a freeware utilities package that works with the phylogenetic inference package Phylip |
| tree-puzzle 5.2 |
a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. |
| Archaeopteryx 0.957b |
a Java tool for the visualization of annotated phylogenetic trees |
| TREECON 1.3b Demo |
a software package developed primarily for the construction and drawing of phylogenetic trees |
| COMPONENT 2.0 |
program for analysing evolutionary trees |
| NJplot 2.3 |
a tree drawing program able to draw any phylogenetic tree |
| MEGA 5.05 |
Molecular Evolutionary Genetics Analysis |
| TreeSAAP 3.2 |
Selection on Amino Acid Properties |
| mesquite 2.74 |
software for evolutionary biology |
| PAL 1.51 |
Analysis Library A Java library for molecular evolution and phylogenetics |
| Vanilla 1.2 |
a collection of command line programs written in Java to access some selected features in PAL |
| SplitsTree 4.11.3 |
application for computing evolutionary networks from molecular sequence data. |
| TCS 1.21 |
a Java computer program to estimate gene genealogies including multifurcations and/or reticulations (i.e. networks). |
| GEODIS 2.6 |
a program for the calculation of the statistics and associated P-values for the nested clade analysis (NCA) developed by Templeton and collaborators. |
| RDP 3.44 |
Recombination detection program |
| FastME 2.0.7 |
a distance based phylogeny reconstruction algorithm. |
| REAP |
an integrated environment for the manipulation and phylogenetic analysis |
| T-REX 4.01 |
Tree and Reticulogram reconstruction |
| FSTAT 2.9.3.2 |
a computer package for PCs which estimates and tests gene diversities and differentiation statistics from codominant genetic markers |
| ProfDist 0.9.9 Beta |
A tool for the construction of large phylogenetic trees based on profile distances |
| STC 1.2 |
a new distance-based clustering method, triplet clustering algorithm |
| SymmeTREE |
tests of differential diversification rates |
| PVT |
Phylogenetic Visualization tool |
| TREEFINDER 201103 |
computes phylogenetic trees from molecular sequences. |
| PHASE 2.0 |
a software package for PHylogenetics And Sequence Evolution |
| BAMBE 2.02b |
Bayesian Analysis in Molecular Biology and Evolution |
| jMODELTEST 0.1.1. |
phylogenetic model averaging |
| MrMtgui 1.01 |
a windows and linux interface for modeltest. |
| Clann 3.13 |
determining the optimal phylogenetic supertree |
| Phylogenetic Independence 2.0 |
to conduct the Test For Serial Independence (TFSI) on continuously valued characters and the Runs Test on discretely valued characters (Abouheif 1999) |
| Jevtrace2 v3.15 |
a java implementation of the evolutionary trace method |
| NimbleTree 2.6 |
program for making phylogenetic trees starting from sequence data |
| Phyl-O-Gen 1.1 |
implements some straight-forward birth-death models for simulating phylogenies |
| BEAST 1.6.1 |
cross-platform program for Bayesian MCMC analysis of molecular sequences |
| MESA 1.9.23 |
Macroevolutionary Analysis & Simulation |
| TreeJuxtaposer 2.1 |
Compare phylogenetic evolutionary trees interactively and automatically |
| TreeExplorer 2.12 |
display a phylogenetic tree in several different styles |
| TreeMe 07/2008 |
a comprehensive phylogenetic tree visualization and manipulation software |
| DNATREE 1.3 |
a computer program that simulates the branching of an evolutionary tree |
| Genie 3.0 |
Genealogy Interval Explorer |
| Pebble v1.0 |
Phylogenetics, Evolutionary Biology, and Bioinformatics in a moduLar Environment |
| ArboDraw |
a program for building and displaying phylogenetic trees |
| MrBayes 3.1.2 |
a program for the Bayesian estimation of phylogeny, |
| Network 4.600 |
software for generating evolutionary trees and networks , |
| PhyDE 0.9971 |
Phylogenetic Data Editor |
| PRAP 2.0b3 |
software for Parsimony ratchet analyses with PAUP. |
| CopyCat 1.14 |
provides an easy and fast access to cophylogenetic analyses |
| Dendroscope 3.1.1 beta |
An interactive viewer for large phylogenetic trees |
| TreeGraph 2.0.47-206 beta |
A graphical editor for phylogenetic trees. |
| SeqState 1.41 |
Primer design and sequence statistics for phylogenetic DNA data sets |
| CDTree 3.1 |
A tool to aid in the classification & evolutionary relationships of protein sequences. |
| TreeDyn 198.3 |
Dnamic graphics and annotations for phylogenetic or classification trees analyses . |
| Baobab 3.31 |
An editor for large phylogenetic trees written in Java. |
| Bosque 1.7.157 |
A graphycal software to perform phylogenetic analyses. |
| DoubleTree 0.7 |
An application for comparing two trees using coupled interaction. |
| PoInTree 1.0.1.2 |
An application that allows to build, visualize and customize phylogenetic trees. |
| figtree 1.3.1 |
A graphical viewer of phylogenetic trees. |
| DensiTree 2.0 |
A program for qualitative analysis of sets of trees. |
| Leaphy 1.0 |
Likelihood estimation algorithms in phylogenetics. |
| Phylodendron 0.8d |
Phylogenetic tree drawing. |
Plasmid Map |
|
| NoeClone 3.0 Demo |
Virtual cloning laboratory. |
| pDRAW32 1.1.112 |
Scientific software for the molecular biologist |
| CloneMap 2.16 Demo |
solution for fast and easy plasmid map drawing,restriction site mapping, and virtural cloning |
| SimVector 4.60 Demo |
tool for drawing publication and vector catalog quality maps |
| ApE 2.0.39 |
A Plasmid Editor |
| BVTech Plasmid 5.1 Demo |
DNA plasmid drawing software |
| Plasm 2.0.4.29 |
A plasmid drawing software. |
| XPlasMap 0.99 |
a DNA mapping program for Mac OS |
| CGView 1.0 |
Circular Genome Viewer |
| PlasmaDNA 1.4.2 |
A free, cross-platform PLAsmid MAnipulation program |
| Plasmidomics 0.2 |
Plasmid Drawing Program. |
Image Analysis |
|
| ImageTool (IT) 3.0 |
a free image processing and analysis program |
| ImageJ 1.45 |
Java image processing program |
| Fiji 20110307 |
An image processing package. |
| Cross Checker 2.91 |
PC software package, developed for analysis of genetic fingerprints such as RFLP, RAPD and AFLP |
| Band Leader 3.0 |
Image analysis software for Gel Electrophoresis samples |
| OSIRIS 4.19 |
a viewer for Papyrus / DICOM images |
| Melanie Viewer 7.0 |
visualize gels and related data obtained through the use of the full version of ImageMaster 2D Platinum or Melanie by colleagues. I |
| TotalLab 12 |
software range for the fast and accurate analysis of 1D gel images. |
| QuantiScan 3.0 Demo |
software to analyze a wide variety of material including polyacrylamide and agarose gels |
| Engauge Digitizer 4.1 |
digitizing software converts an image file showing a graph or map, into numbers. |
| Graph Digitizer 2.16 |
for digitization of orthogonal graphs |
| Peak Explorer 2.11 |
for automatic processing of spectra and also any plots having strongly expressed local maxima (peaks). |
| Volocity Demo 5.5.1 |
A feature-filled, user friendly software product, provided free of charge to scientists |
| GetData 2.24 |
a program for digitizing graphs and plots. |
| Bersoft Image Measurement 7.2 |
application that makes it easy to acquire, measure, and analyze digital images |
| DigitizeIt 1.5 |
software replaces a digitizer tablet. |
| CellC v1.2 |
software for quantification of labeled bacteria by automated image analysis. |
| Grid cell counter 0.9.9.8 |
Display a grid over your image. |
| BioImageXD Beta r1537 |
free open source software for analysis, processing and 3D rendering of multi dimensional microscopy images. |
| CoPlot 6.4 |
Program for making publication-quality 2D and 3D scientific graphs. |
| CP ATLAS 2.0 |
Cross-Platform Advanced Thin Layer and Gel Analysis Software. |
| Gel Analyzer 2010a |
1D gel electrophoresis analysis software . |
| TMAJ 3.4.0 |
Software for Tissue MicroArrays (TMA's). |
| GelQuest 3.0.4 |
Software for the analysis of DNA fingerprints. |
| TinyQuant v1.55 |
A miniature utility for gel image analysis. |
| V3D 2.603 |
3D/4D/5D Image Visualization & Analysis System for Bioimages |
| AxonTracker 1.0 |
3D software tool. |
| OMERO 4.3.3 |
The Open Microscopy Environment |
| Bio-Formats 4.3.3 |
A standalone Java library for reading and writing life sciences image file formats. |
| VisBio 3.40rc1 |
Biological visualization tool. |
Alignment |
|
| Geneious 5.5.5 |
genome & proteome research tools |
| MACAW 2.05 |
Multiple Alignment Construction & Analysis Workbench |
| Clustal W 2.1 |
multiple alignment program for DNA or proteins. |
| FASTA 36.3.5b |
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. |
| GeneDoc 2.7.0 |
A Full Featured Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows. |
|
BLAST 2.2.25 |
The Basic Local Alignment Search Tool |
| SeqPup 0.9 |
a biological sequence editor and analysis program |
| K-Estimator 6.1v |
a program to estimate the number of synonymous (Ks) and nonsynonymous substitutions (Ka) per site. |
| BioEdit 7.1.3 |
a biological sequence alignment editor written for Windows 95/98/NT/2000/XP. |
| DAMBE5.2.31 |
Data Analysis and Molecular Biology and Evolution software |
| SeaView 4.3.3 |
a graphical multiple sequence alignment editor |
| Jalview 2.7 |
a multiple alignment editor written entirely in java |
| DNASIS Max trial 3.0 |
Bioinformatics software |
| Genamics Expression 1.1 |
a revolutionary new Windows application for DNA and protein sequence analysis. |
| Vector NTI Viewer 4.0.1 |
a freeware program, allows scientists to study and analyze biological molecules. |
| Jellyfish 3.3.1 |
an innovative software tool that provides helpful gene analysis capabilities in an intuitive and easy-to-use interface. |
| ProSeq 3.2 |
program for sequence editing and population genetics (mol/evol) analysis. |
| SMS 2 |
The Sequence Manipulation Suite |
| Staden 2.0.0b8 |
A fully developed set of DNA sequence assembly (Gap4), editing and analysis tools |
| ISYS v1.35 |
a dynamic, flexible open source platform for the integration of bioinformatics software tools and databases. |
| PhyloGrapher2003.4.3 |
a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements) |
| SeWeR 3.0 |
an acronym, stands for SEquence analysis using WEb Resources. |
| WinBlast v.0.2.0 |
a Windows graphical front-end for NCBI BLAST. |
| SeqVISTA 1.81 |
A Graphical Tool for Sequence Feature Visualization and Comparison |
| GENOME EXPLORER 1.0b |
a Java front end to many useful bioinformatics tools |
| PowerBlast 1.2.0 |
Blast local tools |
| JAligner 1.0 |
local pairwise sequence alignment software |
| DNAMAN 7.0 Demo |
sequence analysis tools |
| CLC Sequence Viewer 6.5.3 |
bioinformatics analyses workbench. |
| MAFFT 6.864 |
a multiple sequence alignment program. |
| Exonerate 2.2 |
a multiple sequence alignment program. |
| Lalnview 3.0 |
graphical program for visualizing local alignments between two sequences |
| NeoBio 1.0 pre-alpha |
Bioinformatics Algorithms in Java |
| STRAP 20111124 |
Multiple Sequence Alignment Interactive Program |
| Mauve 2.3.1 |
Genome Alignment Software |
| Laj 070222 |
tool for viewing and manipulating the output from pairwise alignment programs |
| YASS v1.14 |
DNA local alignment tool |
| Utopia 1.4.5 |
Molecular Structure Viewer and Colour INteractive Editor for Multiple Alignments |
| GENtle 1.9.4 |
a software for DNA and amino acid editing |
| Align-m v2.3 |
multiple alignment software |
| QAlign 2.60.80 |
Multiple alignment and editor software. |
| seqtools v. 8.4.066 |
tools for basic and advanced analyses of nucleotide and protein sequences. |
| BlastViewer 2.3 |
software to explore BLAST results graphically |
| CGViz 1.3.5 |
highly flexible framework for designing biomolecular viewers. |
| BioSeqAnalyzer 1.0 demo |
a bioinformatics software tool for analyzing DNA and protein sequences. |
| Topali 2.5 |
statistical and evolutionary analysis of multiple sequence alignments. |
| IGV 2.0.34 |
A visualization tool to simultaneously integrate and analyze multiple types of genomic data. |
| EMBOSS 6.4.0.4 |
The European Molecular Biology Open Software Suite |
| Biskit 2.3.1 |
A Python platform for structural bioinformatics. |
| geWorkbench 2.2.2 |
genomics Workbench , a Java-based open-source platform for integrated genomics. |
| SnS-Align |
Structure and Sequence Alignment Software. |
| UGENE 1.10.1 |
Integrated Bioinformatics Tools. |
| CHROMA1.0 |
A tool for generating annotated multiple sequence alignments. |
| Recco 0.93 |
Recombination Analysis Using Cost Optimization. |
Bio-chip |
|
| ScanAlyze 2.51 |
Process fluorescent images of microarrays |
| Cluster 2.20 |
Perform a variety of types of cluster analysis and other types of processing on large microarray datasets. |
| TreeView 1.60 |
Graphically browse results of clustering and other analyses from Cluster |
| ArrayMaker 2.6 |
provides high performance robotic control of microarrayer robots |
| J-Express pro 2011 |
software package for analysis and visualization of microarray data |
| MAExplorer Version 0.96.34.01 |
Java-based data-mining facility for cDNA or oligonucleiotide microarray databases |
| FreeView & FreeOView |
programs for viewing and optimizing gene expression dendrograms |
| dchip 2010.01 |
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 |
| SAM 4.00 |
Significance Analysis of Microarrays |
| BRB-ArrayTools 4.2.0 |
visualization and statistical analysis of DNA microarray gene expression data |
| AMIADA 2.0.7 |
program for organizing, exploring, visualizing, and analyzing microarray data |
| DNA_MAP 1.0 |
DNA Macroarrays Analysis Program |
| GalFileGenerator v1.4 |
Conversion of a file of 96 well plates into a file of 384 well plates, and conversion of a file of 384 well plates into an Axon GenePix Gene Array List file |
| Array-A-Lizer 1.03 |
expedient determination of the quality of multiple spotted DNA microarray experiments |
| cluster 3.0 10.12.27 |
enhanced version of Cluster |
| GenePattern 3.3.3 |
analytic tools for genomic data |
| GenMAPP-CS 0.2 |
Gene Map Annotator and Pathway Profiler |
| MADAM v4.0 |
primary data entry, tracking, and reporting system. |
| Spotfinder v3.2.1 |
multi-channel image analysis tool for microarray images |
| MIDAS 2.22 |
a normalization and filtering tool used to process the raw data output from Spotfinder |
| MeV 4.8 |
main data analysis and visualization tool for microarray |
| TreeArrange |
program for reordering and displaying expression array data. |
| Java Treeview 1.1.6r2 |
Viewer for Microarray Data in the PCL or CDT format |
| EXPANDER 6.0 |
EXpression Analyzer and DisplayER |
| OligoArray 2.1.3 |
a program that computes gene specific oligonucleotides that are free of secondary structure for genome-scale oligonucleotide microarray construction. |
| BAGEL 4.1.1 |
Bayesian Analysis of Gene Expression Levels (BAGEL): a program for the statistical analysis of spotted microarray data. |
| CAGED 1.1 |
a computer program for the analysis of temporal gene expression data. |
| GAAS 1.0.0.1 |
Gene Array Analyzer Software |
| GLR 1.0 |
a statistical analysis program to identify differentially expressed genes from microarray data |
| NIA Array Analysis Tool 2.0 |
Statistical analysis is based on the single-factor ANalysis Of VAriance |
| tools for microarray |
tools for microarray |
| UCSF Spot 2.1 |
a program for microarray image quantification |
| ArrayMiner 5.3 lite |
a set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data |
| Venn Mapper 1.01 |
a program that compares heterologous microarray data sets, based on the number of common, differentially expressed genes. |
| MAIA 2.75 Demo |
Microarray Image Analysis Software , |
| MAGIC Tool 2.1 |
MicroArray Genome Imaging & Clustering Tool. |
| Array Tools 3.3 |
Add-In for Microsoft Excel, which is designed to handle the microarray data. |
| Genom 2005 3.42 |
application for analysing array-experiments. |
| Mayday 2.12 |
A workbench for visualization, analysis and storage of microarray data. |
| ChipInspector 2.1 |
software to analysis microarray data. |
| OligoWiz 2.2.0 |
Microarray Probe Designer. |
| ENIGMA 1.1 |
a software tool to extract gene expression modules from perturbational microarray data |
| PermutMatrix 1.9.3 |
Software for gene expression microarray data analysis. |
| KegArray 1.2.3 |
Java application for microarray data analysis. |
| Correlate 1.03 |
An Excel plug-in that performs sparse canonical correlation analysis. |
| Picky 2.20 demo |
Oligo Microarray Design and Analysis |
| ParaSAM |
An application for significance analysis of microarrays using a parallelized algorithm. |
| VIZARD 1.2 |
A Java program for analysis and visualization of Affymetrix GeneChip? data. |
| COCAS V2.4 |
A ChIP-on-chip analysis suite. |
| ResqMi 1.2.1 |
Tool for analyzing, viualizing and editing Resequencing Microarray data. |
| ArrayCluster 1.0 |
Mixed Factors Analysis of Microarray Gene Expression Data. |
Miscellaneous |
|
| DynaFit 4.04.064 |
perform nonlinear least-squares regression of chemical kinetic, enzyme kinetic, or ligand-receptor binding data |
| Migrate-N 3.2.16 |
estimates effective population sizes and past migration rates |
|
arlequin 3..5.1.3 |
exploratory population genetics software |
| FBAT 2.0.4 |
FBAT --Family Based Association Testing software |
| GGT 2.0 2010 |
for Graphical GenoTypes |
| CERVUS 3.0.3 |
program for assignment of parents to their offspring using genetic markers |
| SBW 2.8.3 |
The Systems Biology Workbench |
| Gepasi 3.30 |
software package for modeling biochemical systems |
| DBsolve c8 |
DBsolve - software for metabolic simulation after genome sequencing |
| boxit 2007 DEMO |
collect, store and organize information about all your antibodies |
| GRR 1.2.1.41 |
application for detecting pedigree errors via graphically inspecting the distribution for marker allele sharing among pairs of family members or all pairs of individuals in a study. |
| AceDB 4.9u |
a genome database designed specifically for handling bioinformatic data |
| MAPL98 / DIAL98 / GEST98 |
Statistical Genetics software |
| PED 6.0.2 |
interactive pedigree drawing software |
| PEDRAW 2.5 |
Pedigree Drawing Software |
| MassXpert 3.1.0 |
a mass spectrometric program for predicting and analysing mass spectrometric data obtained on proteins and peptides. |
| WinMDI ver 2.9 |
WinMDI (Windows Multiple Document Interafce for Flow Cytometry) |
| TestDNA |
a utility that generates FCS histograms of cell cycle data with known component values. |
| Flow Cytometer Simulator |
This application provides a simulation of a working flow cytometer |
| FCS File Mixer Sanitizer |
merge 2 or more FCS listmode files into a new file. |
| E-Cell 3.2.2 |
a concept of constructing virtual cells on computers |
| WEASEL 3.0.2 |
flow cytometry data analysis and display program |
| FCSM |
Frozen Cell Stock Monitor software |
| MICE 1.4 |
Mouse Information and Classification Entity software, |
| REtools 5.0 |
a program to assist in restriction enzyme use |
| PEDIGREE VIEWER 6.5b |
Draws and manipulates pedigree diagrams. |
| ezFreezer 1.4.5 Demo |
samples and specimens management software. |
| FCSExpress V4 Demo |
Flow Cytometry Data Analysis software. |
| BioDownloader 2.2.1.0 |
a program for downloading and/or updating files from ftp/http servers |
| Cytoscape 2.8.2 |
bioinformatics software platform for visualizing molecular interaction networks. |
| Taverna 2.3 |
software tools to facilitate easy use of workflow and distributed compute technology. |
| APP 2.28 |
Advanced Pathway Painter. |
| EPE 3.0a13 |
Edinburgh Pathway Editor. |
| MetaPAT 07.02 |
A Tool for the Alignment of Metabolic Pathways |
| InforBIO V5.28 |
e-Workbench for databasing, classification and identification of microbes. |
| Labmatica 1.7brc2 |
Free Laboratory Information Management System. |
| Flow Explorer 4.2 |
Flow cytometry programs |
| FlowJo7.6.5 |
Flow Cytometric analysis programs |
| LDATAPP 2.0 |
Dumps FCS listmode or histogram data into ASCII text files. |
| cytowin 4.31 |
Flow cytometry software. |
| Haploview 4.2 |
Designed to simplify and expedite the process of haplotype analysis. |
| MarVis Suite 1.0 |
Clustering and Visualization of Metabolomic Markers |
| Arcadia 1.0rc2 |
A visualisation tool for metabolic pathways. |
| GRaPe 1.0 |
Gene Reaction Protein Builder |
| VersaCount 1.02 |
An application to assist with the counting of cells by microscopy. |
| Cell Counter 3.2 |
A program for counting cells (or other things). |
| ListMath 2.1 |
Flow Data List Files Analysis software. |
| GOLD 1.1 |
Software package that provides a graphical summary of linkage disequilibrium. |
| MetNetMaker 1.5.2 |
Software to create metabolic networks. |
| GNLab |
Computational Pipeline for Large-Scale Gene Network Analysis. |
| GenAlEx 6.41 |
Genetic Analysis in Excel. |
| BioNetBuilder 2 |
Cytoscape plugIn that create biological networks. |
| GSearcher 1.4 |
Cytoscape plugin that offers a high performance searching |
| GLay |
Cytoscape plugin that offers an assorted collection of community analysis algorithms. |
| BioTapestry 5.0.2 |
An interactive tool for building, visualizing, and simulating genetic regulatory networks. |
| BRM 2.2 |
Bioinformatics Resource Manager |
| Mendel v11.0 |
Comprehensive Package for Statistical Genetic Analysis. |
| SimWalk 2.91 |
A statistical genetics computer application |
| BayeScan 2.01 |
Detect Natural Selection from Population-base Genetic Data. |
| PBAT 3.67 beta |
Pedigree Based Association Testing. |
| CADLIVE 2.75 |
Computer-Aided Design of LIVing systEm. |
Chemical Draw |
|
| ACD/ChemSketch 12.0 |
advanced chemical drawing tool |
| Accelrys Draw 4.0 |
chemically intelligent drawing package |
| Marvin 5.5.0.1 |
Java based chemical drawing tool. |
| ChemFormatter 1.2.5 |
add-in program for Microsoft Office. ChemFormatter automatically applies font styles in a chemical document |
| Chemistry 4-D Draw 8.0.2 Demo |
chemistry program combining the most advanced technologies in structure drawing |
| JChemPaint 3.0.2 |
an editor for 2D molecular structures. |
| ChemDraw Ultra 12.0 Trial |
the software used by scientists to draw structures.SERIAL NUMBER: 026-009370-0367. |
| TinkerCell 20110623 |
A free and open-source computer-aided design (CAD) software for synthetic biology. |
| WinDrawChem 1.6.2 |
Freeware two-dimensional molecule drawing program. |
| ChemDoodle 3.3.1 |
A fully functional chemical drawing application. |
| ChemicPen 2.6 |
Easy to use software for drawing 2D chemical formulae and reactions. |
| WinPLT 7.1.16 |
A program for drawing chemical structures. |
| BKChem 0.14.0-pre2 |
Free, portable, and open-source structure drawing program. |
| KegDraw 0.1.11b |
Java application for drawing compound and glycan structures |
| JME Molecular Editor 20100102 |
A Java applet which allows to draw / edit molecules and reactions |
| JChem for Excel 5.5.1 |
The plugin to integrate structure handling and visualizing capabilities within Excel. |
Interesting Stuff |
|
| Life32 2.16 |
a player for Conway's game of life. |
| Primordial Life 3.21 |
Experience life and death in a window or as a screen saver! |
| breeder 3.0 |
an entertaining plant breeding game. |
| Cafun 1.0 |
to create impressive simulations of complex systems. |
| Molecular Expressions |
screen saver offers individuals a tremendous amount of variety. |
Irving Geis SS
|
a "screen saver" of images by Irving Geis. |
| cyclovir.exe |
Screen saver demonstrating DNA chain termination caused by Acyclovir. |
| ProteinMusic 1.1 |
converting DNA sequences into music. |
| MP 2.0 |
Molecular Probes Screensaver . |
| Folding@home 6.23 |
a distributed computing project. |
| 3D BioMolecula ScreenSaver 1.1 |
This 3D screensaver shows real 3D models of biological molecules in dynamics. |
| Living Cell 3D Screensaver 1.3 |
Do you want to see what goes on inside living cells. |
| 3D CHEMICAL ELEMENTS SCREENSAVER |
the smartest interactive Periodic Table and 3D Atom Modelling software . |
| INSIDE THE CELL 3D |
Inside the Cell 3D screensaver will provide you with a unique opportunity to plunge into the very depths of the living organism. |
| Pus-Poppin Frogs 1.0.1 |
a game about SNP and side effort. |
| VEM |
Virtual Electron Microscope . |
| Microbworld |
Microbiology Screensaver . |
| Bio2MIDI v2.1 |
converts the text of a DNA or protein sequence to a MIDI file . |
| Bugs 2.0 |
program that simulates bacteria-like organisms. |
| Binary |
fills your screen with scrolling C/G/A/T. |
| Gene Pool 6 |
artificial life simulation. |
| Darwin Pond |
artificial life simulation. |
| Dna-baser screen saver |
Screen Saver. |
| brscreen |
BRAINY SCREEN SAVER. |
| biogenesis 0.8 |
the software simulates in a visual fashion the processes involved in the evolution of unicellular organisms at nature, |
| DNA2ABC 1.0.1 |
a Tcl/Tk application for turning DNA sequences into musical sequences. |
| DNA Ball 1.5 |
Gaming software. |
| D.N.A. |
Addictive puzzle game. |
| Foldit |
A revolutionary new Protein fold computer game. |
| Rosetta@home |
Software to determine the 3-dimensional shapes of proteins. |
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