Free graph visualization library software for linux

The Visualization ToolKit (VTK) is an open source, freely available software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. Visualization Toolkit consists of a C++ class library, and several interpreted interface layers including Tcl/Tk, Java, and Python.
Professional support and products for VTK are provided by Kitware, Inc. VTK supports a wide variety of visualization algorithms including scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as implicit modelling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. In addition, dozens of imaging algorithms have been directly integrated to allow the user to mix 2D imaging / 3D graphics algorithms and data.
The design and implementation of the library has been strongly influenced by object-oriented principles. VTK has been installed and tested on nearly every Unix-based platform, PCs (Windows 98/ME/NT/2000/XP), and Mac OSX Jaguar or later.
Many resources exist to help you utilize the full potential of VTK in your application area. These resources include:
Mailing List: Over 1900 users are subscribed to this list. A great place to post questions, and search for answers.
VTK Textbook: The Visualization Toolkit, An Object-Oriented Approach To 3D Graphics, 3rd edition, ISBN 1-930934-12-2, now published by Kitware. This is a great book to read if you want to learn the details of the visualization algorithms and data structures. The book is often used as a college text in visualization and graphics courses.
VTK Users Guide: The Visualization Toolkit Users Guide, ISBN 1-930934-13-0, published by Kitware. This is the book to get if you want to learn how to install and use VTK.
ParaView Guide: The ParaView Guide, ISBN 1-930934-14-9, published by Kitware. ParaView is a turn-key visualization system build on top of VTK, and makes VTK easier to use with an interactive, point and click interface. ParaView also supports supercomputing applications, including tiled display and distributed parallel processing.
CMake: Mastering CMake, ISBN 1-930934-11-4, published by Kitware. CMake is the premier, cross-platform build system used to compile and link VTK. A useful book if you want to use VTK in your projects.
Support: A variety of support options are available ranging from the single point-of-contact Professional Subscription to get you up and running, to custom Site Support to help you develop your next product with VTK.
Enhancements:
- Many bugs were fixed, including fixes for memory leaks, array bounds errors, and stack overflows.

Genomorama: Genome Visualization is a multi-scale, multi-genome, multi-platform visualization and analysis program. It provides a powerful yet easy to use interface that leverages the visualization power of modern computers (via OpenGL) and the substantial bioinformatic infrastructure provided by the NCBI (via the NCBI C toolkit).
Genomorama is written in portable, highly optimized C++ and comes in three "flavors" that allow it to run natively on (most) modern operating systems: OS X (using Carbon), Microsoft Windows (using MFC), and Linux (using Motif). Executables and source code are freely provided for all flavors.
Main features:
- High performance has not been sacrificed on the altar of portability
- OpenGL graphics take advantage of the video-game optimized graphics cards available in most desktop and laptop computers.
- C++ allows transparent and complete utilization of system resources (like memory).
- Native windowing toolkits (Carbon, MFC and Motif) for every operating system facilitate responsiveness and ease of use.
- A stand-alone, self-contained executable frees Genomorama from dependence on third party applications.
- Source code for all platforms is freely available.
- An attractive, full featured user interface
- Genomorama presents a clean, uncluttered user interface.
- Multi-scale rendering displays relevant details while maintaining readability.
- Use a keyboard or a mouse to efficiently zoom, pan and explore genomes of arbitrary size.
- Attractive WYSIWYG Postscript and GIF output formats yield publication quality images.
- Novel features to aid genome analysis
- In addition to the standard searching options (like query by sequence and gene name), Genomorama offers "forward and reverse" DNA hybridization based searches.
- Provide a pair of PCR primers, and Genomorama will output the amplicons.
- Provide a hybridization probe and Genomorama will find binding sites.
- Provide a pair of Padlock probes and Genomorama will identify binding locations
- Provide a set of PCR primer criteria (length, melting temperature, base composition, etc.) and Genomorama will find PCR primers.
- Genomorama can display and search an arbitrary number of genomes (limited only by computer memory).
- Harness the power of the NCBI toolkit to directly access and search the NCBI Entrez database.
- Compute melting profile, in addition to traditional base composition plots (i.e. %G+C, %A+T, etc).
Enhancements:
- This release fixes the following bugs: parsing gbk files that contain single base annotations on the complement strand;
- missed exact matches at 3 end of target sequence;
- fragile parsing of annotation range;
- downloading of very large Genbank records (i.e. human chromosomes);
- and omitted intergenic space following single base annotations (i.e. SNPs).
- Custom color records are now saved to and read from GBK files.
- An OS X Intel-specific executable has been added.
- The information dialog box has been made resizable.

The Configuration File Library (CFL) is a collection of routines for manipulating configuration files. The project is a portable library fully written from scratch in pure ANSI C.

It is designed to offer for C programmers common routines for manipulating configuration text files.

Redland RDF library is a set of free software packages that provide support for the Resource Description Framework (RDF).
Main features:
- Modular, object based libraries written in C.
- APIs for manipulating the RDF graph, triples, URIs and Literals.
- Triple sequences for efficient streaming.
- Parsers and Serializers for reading and writing RDF as RDF/XML, N-Triples and Turtle Terse RDF Triple Language syntaxes via the Raptor RDF Parser Toolkit.
- Storage for graphs in memory, with Sleepycat/Berkeley DB, MySQL 3/4, AKT Triplestore, SQLite, files or URIs.
- Querying with RDQL and SPARQL using the Rasqal RDF Query Library.
- Redland contexts for managing data aggregation and recording provenance.
- Language Bindings in C#, Java, Obj-C, Perl, PHP, Python, Ruby and Tcl via the Redland Bindings package.
- Command line utility programs rdfproc (RDF), rapper (parsing) and roqet (query).
- Portable, fast and with no known memory leaks.
Enhancements:
- The code was updated to use Rasqal RDF query library 0.9.14 and Raptor RDF parser/serializer library 1.4.15.
- A new transaction API was added, implemented with MySQL for consistent changes to the graph.
- A new query results formatter class was added.
- Many other bugs were fixed.

CVS Perl library is a Perl module which is a wrapper around the CVS command with an object-oriented interface.

Installation:

To install this module type the following:

perl Makefile.PL
make
make test
make install

Quantity/Formatter Library provides a Java library made with the quantity/formatter pattern..

Quantity/Formatter Library is a Java library developed in accordance to the quantity/formatter pattern (as demonstrated by the Date/SimpleDateFormat in the standard J2SE library).

The following quantity/formatter pairs are currently available:

Currency/CurrencyFormat,
Density/ DensityFormat,
Dimension/DimensionFormat,
Distance/ DistanceFormat,
ElapsedTime/ElapsedTimeFormat,
Temperature/TemperatureFormat,
Volume/VolumeFormat
Weight/WeightFormat.

SAgl is a portable small antialiased graphics library. It offers lines, circles, and bezier curves, as well as thick lines and fills.

It can be used on top of SDL or with X or any other graphics system.