WINDOWS

AminoXpress software offering 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 etc.
Artemis : Java based DNA sequence viewer and annotation tool.
Antheprot  permits the analysis of a protein sequence and 3D structure analysis.
BioEdit  : Sequence/alignment editor able todo  translations, phylogenetic analysis, clustalw alignments, ABI trace analysis, RNA comparitive analysis and BLAST searches
Blast Client Software(Network) Basic Local Alignment Search Tool. 
Blast (stand alone version)
Boxshade  Prints and Shade  Multiple-Alignment files.
Chem2Pac  computational chemistry integrator
Chime Plug-in This will allow you to visualize pdb files over the net.
CIFters :Tools for manipulating Crystallographic Information Files
ClustalW sequence alignment program
Codontree : Codontree plot codon usage table for a set of protein coding genes, gene relationship on the basis of codon usage similarity, and compositional features of protein coding genes.
ConsInspector 3.0:  ConsInspector predicts potential binding sites in sequences of unlimited length by comparing candidates with predefined consensus descriptions of protein binding sites.
Coresearch  : Program is used to identify and delimitate consensus elements (e.g. protein binding sites) in a set of unaligned nucleic acid sequences.
Compare3D Compare3D is used to analyze the structure alignment of two or more polypeptide chains. The alignment is provided by the user, and is thus designed as a visual front end to another program.
Deep Viewer Tools for analysis of  several proteins at the same time.
DNATools  Comprehensive software package for analysis of DNA and protein sequences. offer  programs like  blast, formatdb, clustalw, clustalx, genedoc
DOTPackage for examining molecular interactions
EQS4WIN Lite This  software  allows thermodynamic equilibrium computation
Fasta Fast Alignment Search Tool.
Flex Program which shows molecules and animation sequences
GeneDoc Multiple sequence alignment editor.
GeneStudio LE: Free version of the upcoming Gene Studio Pro.
GeneTool : This  is a DNA sequence analysis package that offers a single, integrated environment in which to rapidly search public and proprietary databases, probe sequence homologies, access functional information, align multiple sequences and produce publication quality graphics.
GeneTree Tool  for comparing gene and species trees.
gOpenMol graphical  interface to the OpenMol
Macaw  program  for locating, analyzing, and editing blocks of localized sequence similarity among multiple sequences and linking them into a composite multiple alignment.
Mage (Version 5.4) Three dimensional viewing of molecules.
MICE Molecular Interactive Collaborative Environment project page.
MMQL A C++ class library, for querying features of biological macromolecules.
MOLMOL Program for viewing  3D structure  of molecules.   
Net-Entrez  is an important tool for search the various sequence databases and the protein database.
Octopus  This is a  merger program  of Visual BLAST-II and Visual FASTA.
pdb2pov  Program  to convert pdb formatted files to povray.
PDBViewer  This is a  three-dimensional viewer. 
pDRAW32 This software is used for annotations, DNA cloning, sequence editing, analysis, enzyme selection, and various outputs.
PDVIN-Protein Data Viewer.
Phylip Phylogeny inference package.
Plasmid 1.0 :  Draw  sequence maps and perform DNA sequence analysis.
PrestoPlot  A 2D plotting tool.
Protein Explorer Program to explore 3D structure of proteins, DNA, RNA.
PSAAM Protein Sequence Analysis and Modeling package.
PDBlib C++ class library for representing a protein structure.
Qmol: Program to view  molecules.
QuickPDBJava applet for viewing PDB structures.
Rasmol 2.7.1 This is a  universal molecular modeling program.
Redasoft Visual Cloning 2000  Program for genetic map drawing and DNA sequence analysis.
RDP : Program for analysing recombination amoungst aligned DNA sequences.
RNAdraw: Program for RNA secondary structure calculation and analysis.
SecTrace is designed to draw pictures ready for publication from secondary structure prediction.
Seqverter 1.3 program to convert sequence file format.
Shape : Package for analysis of molecular surfaces.
Spectrum is a program designed to read in a data file comprising aligned sequences.
STING Tool for the simultaneous display of information about macromolecular structure.
Swiss-PdbViewer provides a user friendly interface  to analyse several proteins at the same time.
TREEMAP Compares host and parasite trees.
TREEVIEW   NEXUS or PHYLIP tree file viewer .
XtalViewPackage for X-ray crystal structure solution.
WPDB PC based software version of PDB.

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MAC

Artemis :Java based DNA sequence viewer and annotation tool.
Blast Client Software
Chime Plug-in - This will allow you to visualize pdb files over the net. 
Deep Viewer provides you friendly interface allowing to analyse several proteins at the same time.
Gene Inspector 1.5 :A combination of a versatile electronic laboratory notebook, a sequence analysis package, and an illustration tool for the Macintosh. This electronic notebook will allow you to plan, organize, and carry-out your experiments.
GeneTool : This  is a DNA sequence analysis package that offers a single, integrated environment in which to rapidly search public and proprietary databases, probe sequence homologies, access functional information, align multiple sequences and produce publication quality graphics.
Macaw  is a software for locating, analyzing, and editing blocks of localized sequence similarity among multiple sequences and linking them into a composite multiple alignment.
Mage Three dimensional viewer of molecules. 
MacBoxshade progran for Shading of Multiple-Alignment files.
MPSA is a program for protein sequence analysis.
NIH-Image image processing and analysis program.
Protein Explorer: cousin of Rasmol but easier than Rasmol .You can view, rotate, explore 3D structure of proteins, DNA, RNA.
RasMol is the universal molecular modeling program. 
Swiss-PdbViewer program that gives a interface allowing to analyse several proteins at the same time.

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UNIX

Artemis :Java based DNA sequence viewer and annotation tool.
Autobodrot, program that explores the Ranges of dihedral angle conformations.
Antheprot  analyse protein sequence and 3D structure.
AQUA :Program for analyzing the quality of biomolecular structures determined via NMR spectroscopy.
Codontree :This program is able to determine a codon usage table for a set of protein coding genes, gene relationship on the basis of codon usage similarity, and compositional features of protein coding genes.
Dang Protein DataBank (PDB) molecular structure file reader.
DomainFinder 1.0 program for the determination and characterization of dynamical domains in proteins.
Flip  : A Unix C program used to find and translate ORF. Flip reformats DNA sequences and produces output files that can be used by other programs such as FASTA.
FTDock,RPScore and MultiDock   software for examining the docking and the interaction between
Garlic molecular visualization program.
GeneMark :This program is meant  for gene prediction in genome sequences. Identifies ORFs, exons, and introns.
GeneTool : This  is a DNA sequence analysis package that offers a single, integrated environment in which to rapidly search public and proprietary databases, probe sequence homologies, access functional information, align multiple sequences and produce publication quality graphics.
Genome Inspector : Detects distance associations between sequence elements.
gOpenMol graphics interface to the OpenMol
Glimmer : Program  for finding genes, using interpolated Markov models to identify the coding regions and distinguish them from noncoding regions, in microbial DNA.
ModelGenerator and ModelInspector : Generate  functional models for transcriptional regulatory DNA units.
Wise2 :A software package that compares DNA sequences at the level of conceptual translation, regardless of sequencing error and introns. It can compare a single protein or a profile HMM to a genomic DNA sequence, and predict a gene structure. sequence analysis.
Probe program to view and score atomic packing of molecules.
Restriction Map Alignment : This program reads restriction maps and deciphers alignments.
SEALS : Software developed  for large-scale research projects in bioinformatics.
Simple34 : It estimates the amount of sequence repetition in nucleotide sequences.
XYLEM :Enable the user to identify, extract and manipulate data from major databases such as GenBank, EMBL and PIR.

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