Artemis is a DNA sequence viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. It can read and write complete EMBL and GENBANK database entries or sequence in FASTA or raw format. Extra sequence features can be in EMBL, GENBANK, or GFF format.
JMV (The Java Molecular Viewer) is a molecule viewer program/component written in Java and Java3D. It is designed to be an easy-to-use, platform neutral molecular visualization tool which can be used standalone or integrated into a larger program. It provides several molecular representations, multiple coloring styles, lighting controls, and stereoscopic rendering capabilities. It loads PDB files over the web, from the RCSB protein databank, from BioCoRE filesystems, and from local filesystems. The interface can be customized by users, and can be disabled for web-based presentations of molecules to save browser space.
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.
slcview allows you to fully script creation of clustergrams and tree diagrams from .cdt, .gtr, and .atr files as output by several biologically-oriented clustering programs, namely Cluster and XCluster. Many options allow you control of the output, and, in addition, slcview allows you to create an annotated legend with the same scale of colors as used in your clustergram.
The libmba package is a collection of mostly independent C modules potentially useful to any project. There are the usual ADTs including a linkedlist, hashmap, pool, stack, and varray, a flexible memory allocator, CSV parser, path canonicalization routine, I18N text abstraction, configuration file module, portable semaphores, condition variables, and more. The code is designed so that individual modules can be integrated into existing codebases rather than requiring the user to commit to the entire library. The code has no typedefs, few comments, and extensive man pages and HTML documentation.
libGenome is a development library designed to make common operations on DNA and protein sequences easy. libGenome provides functionality to read and write sequence and annotation data in several file formats. It provides a common manipulation interface for sequence and annotation data in any supported file format. Some of the basic manipulation functionality offered by libGenome is concatenation, truncation, reverse complementation, and translation of sequences. It was intended to be used on genome size sequences and is optimized accordingly. This is a cross platform library written in ANSI C++ and is currently supported on any platform with gcc. Metrowerks CodeWarrior on Windows and Mac OS are also supported.