Phoenix converts EMBL flat files into some suitable XML format and then read the resulting XML files using whatever XML parser is available in your language.
UNICON is a command-line tool to cope with common cheminformatics tasks. The functionality of UNICON ranges from file conversion between standard formats SDF, MOL2, SMILES, and PDB via the generation of 2D structure coordinates and 3D structures to the enumeration of tautomeric forms, protonation states and conformer ensembles.
fconv is a commandline tool concerning manipulating, converting, and analyzing data from different file formats, such as pdb(qt)-, mol2-, dlg-, cif- and sdf-files.
Linkdatagen is a PERL script that generates LINKAGE style files for ALLEGRO , MERLIN, PREST, MORGAN, PLINK, FEstim, BEAGLE and RELATE using as input genotype calls from Affymetrix SNP chips, Illumina SNP chips, or SNP genotypes inferred from massively parallel sequencing (MPS) data, such as whole exome or whole genome sequence data.
ExpressConverter is a file transformation tool that reads microarray data files in a variety of file formats and generates TIGR MultiExperiment Viewer file (.mev) as output so that the microarray data can be uploaded to the database with MADAM and analyzed with MIDAS and MEV.
GenescanView is the free software for the visualization of files generated with automatic ABI sequencers.GenescanView allows to visualize genescan files (.fsa format from ABI PRISM sequencers) and to view the exact peak size.
PDB Editor (Protein Data Bank ,PDB, File Editor) is a tool for protein crystallographers to expedite selective edit / data extraction / analysis of their PDB files. It allows the user to selectively search, select, extract and edit information in parallel.