General Tools
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Chemaxon: numerous tools for small molecules (standalone).
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DataWarrior: numerous tools (standalone).
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Datagrok Cheminformatics: Cheminformatics functions in Datagrok
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LillyMol: Eli Lilly set of cheminformatic tools (standalone)
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MayaChemTools: Cheminformatics tool kit. A growing collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs (standalone)