ANTHEPROT a package to make protein sequence analysis such as alignment, secondary structure predictions, sites & function detection, physico-chemical profiles, homology search and 3D display of protein structures.

Babel a program designed to interconvert a number of file formats currently used in molecular modeling.

BIONJ a phylogenetic reconstruction algorithm. Improved NJ algorithm.

CHARMM a molecular modelling program.

Chromas a free Windows application which displays and prints chromatogram files from ABI automated DNA sequencers.

CINEMA a Colour INteractive Editor for Multiple Alignments.

ClustalX provides a new window-based user interface to the ClustalW multiple alignment program

ClustalX - parallel a version for SGI/IRIX machines

DRAGON a protein modelling tool using Distance Geometry.

DSSP The DSSP program was designed by Wolfgang Kabsch and Chris Sander to standardize secondary structure assignment.

DynaFit  a program for the statistical analysis and simulation of enzyme kinetic and receptor binding data.

GeneDoc a full featured multiple sequence alignment editor, analyser and shading utility for Windows.

Gepasi 3 Biochemical Kinetics Simulator.

GRAMM Global Range Molecular Matching, a docking program.

GROMOS^TM a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.

HMMER  a package of Hidden Markov models (HMMs) that can be used to do multiple sequence alignment and very sensitive database searching, using statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of HMM software for biological sequence analysis.

ISIS/Draw Preparing reports and presentations, creating structure queries, drawing structures for registration, viewing chemical structures etc. They offer a free license for academic and personal use at home.

LASSAP LArge Scale Sequence compArison Package.

MAPS This is an automated program for Multiple Alignment of Protein Structures

MDL Chemscape Chime Netscape Navigator plug-in that allows scientists to view chemical information directly on an HTML page (A beta is available for Internet Explorer 4).

MELTING computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions.

MEME Multiple EM for Motif Elicitation.

MODELLER homology protein structure modelling by satisfaction of spatial restraints.

MOLMOL MOLecule analysis and MOLecule display.

Molscript a program for creating molecular graphics in the form of PostScript plot files.

Naccess homepage a stand alone program that calculates the accessible area of a molecule from a PDB (Protein Data Bank) format file.

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.

PAML PAML is a program package for phylogenetic analyses of DNA or protein sequences using the method of maximum likelihood

PDB t Multigif PDB2MultiGIF takes the 3D structure and generates an animated image (gif-file).

pDRAW32 a beerware program for DNA cloning, analysis and visualisation.

Phylip free package of programs for inferring phylogenies.

PROCHECK Checks the validity of a 3D structure (bondangles, chirality, bondlengths etc.)

ProFit protein least squares fitting program. It has many features including flexible specification of fitting zones and atoms, calculation of RMS over different zones or atoms, RMS-by-residue calculation, on-line help facility, etc.

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

PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research.

RasMol free software for looking at molecular structures.

RasMol/UMass Amherst another version of Rasmol. Some extra features.

Raster3D a set of tools for generating high quality raster images of proteins or other molecules.

Re_View a 4D-chemical viewer/analyser which is capable of 3D-molecular display, animation (4D-display), geometrical analysis.

SAM Sequence Alignment and Modeling System by Hidden Markov Models

SEALS A System for Easy Analysis of Lots of Sequences) is a software package expressly designed for large-scale research projects in bioinformatics.

SeqPup Document a biological sequence editor and analysis program.

SEQtools is a comprehensive program package for handling and analysis of nucleotide and protein sequences. The program includes a series of trivial functions to help you carry out common operations. In addition SEQtools will assist you with more demanding tasks like unattended batch blast search at NCBI with advanced facilities for retrieving, storing and listing search results.

Swiss-PdbViewer an application that provides a user friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model.

THREADER 2  a program for predicting protein tertiary structure by recognizing the correct fold from a library of alternatives.

TreeView a simple program for displaying phylogenies on Apple Macintosh and Windows PCs.

VMD VMD is a molecular visualization program for displaying and animating large biomolecular systems using 3-D graphics. VMD supports computers running Unix or Windows, is distributed free of charge, and includes source code.

WebLab ViewerLite WebLab® ViewerPro™ is a fully Windows integrated, 3D molecular visualization and chemical communications software package. The high-quality, high-performance OpenGL capabilities allow you to render sophisticated images that before were only available on expensive UNIX workstations