Avogadro is a new, open source molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.
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BioClipse
Bioclipse is a free, open source, workbench for chemo- and bioinformatics with powerful editing and visualization capabilities for molecules, sequences, proteins, spectra etc
BioConductor
Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data.
