- Free DOS version of their excellent F-PROT anti-virus utility. Free for home users. Windows version only gets a free trail version.

Anti-Virus Resources:

     - This is an independent service which will notify you of new releases of the most popular anti-virus software such as McAFEE, Thundbytes, and many others.

Antheprot: 

    - It permits the analysis of a protein sequence and 3D structure analysis.

AminoXpress:

    - A multi-functional biochemsitry software package integrated with modules such as Amino Acid Analysis, Building Block Sort, Digestion, Elemental Analysis, Mass Fragmentation, HPLC Retention Pattern, Isotopic Profile, Combinatorial Library, Molecular Weight, Sequence Parameters, Charge-pH Profile, ... ... The package can be downloaded at http://www.aminoXpress.com (Updated 3/25/01).

Blast Client Software:  

    Basic Local Alignment Search Tool.  It uses amino acid and nucleic acid fragments to search for similarities (Updated 7/16/99).

Boxshade:  

    - Pretty Printing and Shading of Multiple-Alignment files.

Chem2Pac:

    - It is intended to be a kind of computational chemistry integrator, which has a multiple document interface, a molecular rendering utility, and allows the manipulation of various files (Updated 6/16/99).

Chime Plug-in:

    - This will allow you to visualize pdb files over the net.  This program is a necessity if you are a chemist or biochemist Versions 2.0 and Version 1.02. MDL (Updated 4/12/99)

ClustalW: 

    - Is is a powerful tool to do sequence alignments

Deep Viewer: 

    - It is an application that provides a user friendly interface allowing to analyze 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 (Updated 3/25/01).

DNATools: 

    - Comprehensive software package for analysis of DNA and protein sequences. Includes functions for handling small EST projects and a complete set of functions for SAGE analysis. Integrated programs: blast, formatdb, clustalw, clustalx, genedoc (Updated 2/12/00).

EQS4WIN Lite:  

    - It is software that allows thermodynamic equilibrium computation and it is a useful design aid in providing an assessment of the possible behaviors of a complex reacting chemical system at Mathtrek Systems (Updated 5/9/99)

Fasta:  

    - Fast Alignment Search Tool.

GeneDoc:

    - Multiple sequence alignment editor for MS/Windows.

GeneTree:

    - It is an experimental program for comparing gene and species trees. It is available for both Windows and Apple Macs.

ICM lite: 

    - It provides both a command line and graphical interface, allowing the user to take advantage of whichever medium suits their needs best.

MOLMOL:

    - This is a really cool 3D viewer of molecules.  It, however requires a considerable amount of memory to run efficiently

NDE:

    - (NEXUS Data Editor) is a program to create and edit NEXUS format data files on computers running Microsoft Windows 95/NT 4.0.

Net-Entrez:

     - An important tool for search the various sequence databases and the protein database.

Octopus:

     - Alias Visual BLAST release 4.0, is the merger of Visual BLAST-II and Visual FASTA (Updated 9/23/99).

pdb2pov:

     - Molecular Raytracing. This program allows you to convert pdb formatted files to povray.

PDBViewer:

     - It  is a good three-dimensional viewer.  It requires a considerable amount of memory to function properly.

PDVIN:

    -Protein Data Viewer for Windows

Phylip: 

- Phylogeny inference package (Updated 8/20/00).

PrestoPlot:

    - A 2D plotting tool for Win32 Platforms (Windows NT/ME/95/98/00) inspired by Grace/xmgr (Updated 01/29/01). 

Protein Explorer: 

    - View, rotate, explore 3D structure of proteins, DNA, RNA. Much easier to use than RasMol and much more powerful. Clickable sequence-to-structure. Color protein by conservation/mutation from multiple protein sequence alignment (Updated 8/20/00). 

PSAAM:

     - Protein Sequence Analysis and Modeling package used in combination with the Protein Data Viewer for Windows.

Qmol:

    - A lightweight molecular viewer for Windows 95/NT and X Windows (Updated 01/21/01).

RasMol:

   -It  is the universal molecular modeling program.  I would suggest that everyone should have this program because it allows visualization of molecules and it does not require too much memory.  It does require, however, that you know its commands (Updated 5/3/99).

Rasmol 2.7.1:

    - Rasmol 2.7.1 (Latest Version) RasMol version 2.7.0 combined Roger Sayle's version 2.6.4 with Herbert Bernstein's CIF modified version 2.6_CIF(Rev 2) and with Arne Mueller's version 2.6x1.  This site is maintained by Bernstein and Sons (Updated 6/15/99).

Redasoft Visual Cloning 2000: 

-  is an exciting new program for genetic map drawing and DNA sequence analysis that is extensively integrated with the Internet and will greatly improve efficiency and productivity in your lab (Updated 12/11/00). 

RNAdraw:

    - An integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows (Updated 4/7/99)

SecTrace: 

    - is designed to draw pictures ready for publication from secondary structure prediction.

Seqverter 1.3:

    - is a free Windows 95/98/NT sequence file format conversion utility by GeneStudio, Inc. SeqVerter encapsulates a small subset of the features offered by GeneStudio, a complete sequence analysis suite.

Simpip and Simpow:  

    - (MSDOS) a useful group of programs for simulating EPR spectra (Updated 5/13/01).

Spectrum is a program designed to read in a data file comprising aligned character arrays (such as DNA sequence data) or distance data in the form of a matrix, and perform some simple spectral analysis procedures on that data.

STING:

    -It  is a WWW tool for the simultaneous display of information about macromolecular structure (in STING's Graphics Frame) and sequence (in STING's Sequence Frame). Special attention is given to MacroMolecular INTERFACE analysis (Updated 3/25/01).

Swiss-PdbViewer: 

    - is 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 (Updated 3/25/01).