ARB is a graphically oriented package comprising various tools for sequence database handling and data analysis.
BioConductor produces an open source software framework that will assist biologists and statisticians working in bioinformatics, with primary emphasis on inference using DNA microarrays. The team is based at the Biostatistics Unit of the Dana Farber Cancer Institute at Harvard Medical School/Harvard School of Public Health. Participation of interested developers/investigators at other institutions is encouraged. Read more
BioWish is a molecular biology command extension to Tcl/Tk. Features include: sequence statistics, G+C content in different positions, database searches with BLAST, and more.
Crystallography & NMR System: for macromolecular structure analysis.
Fqutils provides a basic set of bioinformatics commandline tools for working with sequence data in FASTQ format.
Intrinsic Noise Analyzer
iNA is a computational tool for quantitative analysis of fluctuations in biochemical reaction networks. Such fluctuations, also known as intrinsic noise, arise due to the stochastic nature of chemical reactions and cannot be ignored when some molecules are present in very low copy numbers only, as is the case in living cells
LabKey Server is open source software that helps scientists manage, analyze, and share complex datasets. It supports tandem mass spectrometry, flow cytometry, assays for neutralizing antibodies,
NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. Read more
SeqPup is a biological sequence editor and analysis program. It includes links to network services and external analysis programs.
UGENE is free open-source cross-platform set of integrated bioinformatics software. Read more