ACEDB
Database system originally developed for molecular biology data

BioBrew
BioBrew Linux is an open source Linux distribution that is enhanced for life scientists. It is customized for cluster and bioinformatics computing. It automates cluster installation, includes all the HPC software a cluster enthusiast needs, and contains popular bioinformatics applications.

BABEL
Interconverting among the many formats used in molecular modeling

BIOML
XML instance for annotating biopolymer sequence information

Bioperl
Collection of Perl tools for computational molecular biology

BioSuite
The bioinformatics division of TCS is currently developing a versatile, portable and comprehensive software product for computational biology

BSML
Bioinformatic structure markup language

CML
SGML extension for managing chemical information

EGO
Performing molecular dynamics calculations on parallel and sequential computers

gOpenMol
Graphical interface to the OpenMol package

MMTK
Program library for molecular modeling applications

Moldy
Molecular dynamics simulation program for simulating atomic, ionic and molecular systems

MolScript
Creating schematic or detailed molecular graphics images

MOPAC
Semi-empirical molecular orbital package for studying chemical structures and reactions

NAB
Language for manipulating macromolecules and their fragmentsa

NAMD
Parallel, object-oriented system for simulating large biomolecular systems

PHYLIP
Performing phylogenices on data such as DNA and protein sequences

PUZZLE
Reconstructing phylogenetic trees from molecular sequence data

RasMol
Molecular graphics for the visualization of proteins, nucleic acids and small molecules

SOLVATE
Constructing atomic solvent environment models for macromodule models, i.e. solutes

spock
Package for displaying protein and nucleic acid structures and searching through related databases

TN-Image
Image analysis program oriented toward molecular biologists, biochemists, and similar beasties

Viewmol
Graphical front-end for visualizing the output of various quantum mechanical and molecular modeling programs

VMD
Program for the visualization and analysis of biological systems, e.g. proteins, nucleic acids, etc.