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PC Software
 | AiO (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). |
| 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). |
| Antheprot permits the analysis
of a protein sequence and 3D structure analysis.
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| Blast Client Software Basic Local Alignment Search Tool. It uses amino acid and nucleic
acid fragments to search for similarities (Updated 7/16/99). |
| Blast (stand
alone version) |
| Boxshade
(Ver. 3.3.1) Boxshade
(Ver. 3.3.1) Pretty Printing and
Shading of Multiple-Alignment files (Updated 10/03/01). |
| Chem2Pac 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).
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| 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)
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| ClustalW is a powerful
tool to do sequence alignments |
| Deep Viewer 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).
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| DICROPROT (DICHROism of PROTeins)
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| 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 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
is an experimental program for comparing gene and species trees. It is available for both
Windows and Apple Macs. |
| Generation 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) |
| gOpenMol 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). |
| ICM 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).
|
| Kinemage (see Mage) |
| Macaw (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. |
| 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 is 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 is a good
three-dimensional viewer. It requires a considerable amount of memory to function
properly. |
| pDRAW32 is used for annotations,
DNA cloning, sequence editing, analysis, enzyme selection, and various outputs (Updated
6/16/99). |
| PDVIN-Protein Data Viewer for
Windows |
| Phylip
Phylogeny inference package (Updated 8/20/00). |
| PrestoPlot:
A 2D plotting tool for Win32 Platforms (Windows NT/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 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).
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| 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). |
|
RasTop 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). |
| 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
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).
|
| TREEMAP is an
experimental program for comparing host and parasite trees. It is available for both
Windows and Apple Macs. |
| TREEVIEW
provides a simple way to view the contents of a NEXUS or PHYLIP tree file. It
includes a TREE
editor. |
| WebLabŪ ViewerLite
brings high quality
molecular graphics to your desktop from Molecular Structure Corporation (MSI). |
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