The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.
JTreeProfiler is a multithreaded Java Profiler with support for Linux, Solaris, and Win32. The result is displayed in a nice TreeMap viewer to locate your time-consuming functions. The results are stored in XML, so they can be formatted by any XML-Tool, like JavaTemplates. The complete methodtraces are recorded for further analysis.
Dar is a shell command that makes backup of a directory tree and files. Its features include splitting archives over several files, DVD, CD, ZIP, or floppies, compression, full or differential backups, strong encryption, proper saving and restoration of hard links, extended attributes, file forks, Door inodes, and sparse files, remote backup using pipes and external commands (such as ssh), and rearrangement of the "slices" of an existing archive. It can run commands between slices, before and after saving some defined files or directories (for a proper database backup, for example), and quickly retrieve individual files from differential and full backups. Several external GUIs exist as alternatives to its CLI interface, like kdar, DarGUI, SaraB, etc.
Image Alchemy has the ability to convert between over 90 different raster image formats (including all colorspace and compression variations of each format). Color management features include gamma correction, undercolour removal, seven high quality dithers, colorspace conversion, and palette manipulation. It also includes a Postscript interpreter.