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bullet  AiOnew.GIF (All in One) is the attempt to integrate a number of standalone programs written between 1987 and 2000 by Christiaan Karreman. They vary between programs that were written purely for database (DB) maintenance and graphic programs depicting plasmids or other DNA. The main advantage of the new AiO is the integration of these programs. Oligos can be designed, ordered via EMail and submitted to the various DBs and visualized immediately in a plasmid map, depicting the exact position and orientation of the new oligo (Updated 10/03/01).
bulletaminoXpressnew.GIF 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).
bulletAntheprot  permits the analysis of a protein sequence and 3D structure analysis.
bulletInformation about Antheprot
bulletBlast Client Software Basic Local Alignment Search Tool.  It uses amino acid and nucleic acid fragments to search for similarities (Updated 7/16/99).
bulletBlast (stand alone version)
bulletBoxshade (Ver. 3.3.1) Boxshade (Ver. 3.3.1) Pretty Printing and Shading of Multiple-Alignment files (Updated 10/03/01).
bulletChem2Pac 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).
bulletmore information
bulletChime 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)
bulletChime Resources by Eric Martz
bulletClustalW is a powerful tool to do sequence alignments
bulletDeep Viewer new.GIFis 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).
bulletDeep Viewer Tutorial by Gale Rhodes (Updated 3/25/01).
bulletDICROPROT (DICHROism of PROTeins)
bulletInformation about DICROPROT
bulletDNATools binoculars.GIF 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).
bulletEQS4WIN Lite 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)
bulletFasta Fast Alignment Search Tool.
bulletGeneDoc Multiple sequence alignment editor for MS/Windows.
bulletGeneTree is an experimental program for comparing gene and species trees. It is available for both Windows and Apple Macs.
bulletGeneration X: a computer simulation of population genetics: (available soon) 1)Gives a better realization of evolution, 2) Illustrates the concepts we learned in class, 3) Shows natural selection in action, 4) Provides insight into population genetics 5) Helps to determine if populations are in Hardy-Weinberg equilibrium 6) Increases understanding about allelic and genotypic frequencies, and 7) Simulation can be repeated until the calculations are memorized at the Department of Biological Sciences, Purdue University. (Updated 7/16/99)
bulletgOpenMol graphics interface to the OpenMol and cand be used for the analysis and display of molecular dynamics trajectories and the display of molecular orbitals, electron densities and electrostatic potentials (4/14/99).
bulletICM lite (registration required) provides both a command line and graphical interface, allowing the user to take advantage of whichever medium suits their needs best (Updated 8/20/00).
bulletKinemage (see Mage)
bulletMacaw  (Version 2.05) is a program for locating, analyzing, and editing blocks of localized sequence similarity among multiple sequences and linking them into a composite multiple alignment. It appears that the last revision was in 1995.
Alternatives Location Comments
Macaw, NCBI NCBI Mirror
Macaw, Sunet Sunet Mirror
Macaw, Indiana Indiana University Mirror
bulletMage (Version 5.4) Three dimensional viewing of molecules.  It is rather primitive by current standards, but it is a good educational tool. This is the official site of kinemage and it is found at Duke University (Updated 5/3/99).
Alternatives Location Comments
Mage, Official Duke University Main site, current version 5.4
Mage, Protein
Protein Science older version 4.2
Mage, FASEB Faseb older version 4.2
Mage, PDB PDB older version 5.28
bulletMOLMOL This is a really cool 3D viewer of molecules.  It, however requires a considerable amount of memory to run efficiently
bulletNDE (NEXUS Data Editor) is a program to create and edit NEXUS format data files on computers running Microsoft Windows 95/NT 4.0.
bulletNet-Entrez  is an important tool for search the various sequence databases and the protein database.
bulletOctopus,  alias Visual BLAST release 4.0, is the merger of Visual BLAST-II and Visual FASTA (Updated 9/23/99).
bulletpdb2pov - Molecular Raytracing. This program allows you to convert pdb formatted files to povray.
bulletPDBViewer  is a good three-dimensional viewer.  It requires a considerable amount of memory to function properly.
bulletpDRAW32 is used for annotations, DNA cloning, sequence editing, analysis, enzyme selection, and various outputs (Updated 6/16/99).
bulletPDVIN-Protein Data Viewer for Windows
bulletPhylip Phylogeny inference package (Updated 8/20/00).
bulletPrestoPlot: new.GIF (3043 bytes) A 2D plotting tool for Win32 Platforms (Windows NT/95/98/00) inspired by Grace/xmgr (Updated 01/29/01). 
bulletProtein Explorer: new.GIF (3043 bytes) 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). 
bulletPSAAM Protein Sequence Analysis and Modeling package used in combination with the Protein Data Viewer for Windows.
bulletQmol: new.GIF (3043 bytes) A lightweight molecular viewer for Windows 95/NT and X Windows (Updated 01/21/01).
bulletRasMol 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).
bulletmain homepage at UMass, Amherst
bulletRasmol 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).
bullet RasTop new.GIF (3043 bytes)is a molecular visualization software for Windows platforms adapted from the program RasMol, initially developed by Roger Sayle. RasTop wraps a user-friendly graphical interface around the "RasMol molecular engine". The software allows several molecules to be opened in the same window and several windows to be opened at the same time. There is no need to type on the command line; each command in the menu generates its own script. Through an extended menu and a command panel, users can manipulate numerous molecules rapidly and learn about them. Work sessions are saved in script format and are fully regenerated with a simple mouse click (Updated 6/16/2).
bulletRedasoft Visual Cloning 2000 new.GIF (3043 bytes) 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). 
bulletRNAdraw: an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows (Updated 4/7/99)
bulletSecTrace is designed to draw pictures ready for publication from secondary structure prediction.
bulletInformation about SecTrace
bulletSeqverter 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.
bulletfor more information about Seqverter
bulletSimpip and Simpow (MSDOS) a useful group of programs for simulating EPR spectra (Updated 5/13/01).
bulletSpectrum 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.
bulletSTING 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).
bulletSwiss-PdbViewer new.GIFis 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).
bulletSwiss PDB Viewer Tutorial by Gale Rhodes (Updated 3/25/01).
bulletTREEMAP is an experimental program for comparing host and parasite trees. It is available for both Windows and Apple Macs.
bulletTREEVIEW   provides a simple way to view the contents of a NEXUS or PHYLIP tree file.  It includes a TREE editor.
bulletWebLabŪ ViewerLite brings high quality molecular graphics to your  desktop from Molecular Structure Corporation (MSI).