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Sequence Quality Control Studio (SeQCoS) is an open source .NET software suite designed to perform quality control (QC) of massively parallel sequencing reads. It includes tools for evaluating sequence and base quality of reads, as well as a set of basic post-QC sequence manip...
The Hidden Markov Model Toolkit (HTK) is a portable toolkit for building and manipulating hidden Markov models. HTK is primarily used for speech recognition research although it has been used for numerous other applications including research into speech synthesis, character recognition and DNA sequencing. HTK is in use at hundreds of sites worldwide.
GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave Forge is a place for development of its packages; from bioinformatics and fuzzy logic to mechanics and instrument control.
Linux Desktop Testing Project is aimed at producing high quality test automation framework (using GNOME / Python) and cutting-edge tools that can be used to test Linux Desktop and improve it. It uses the Accessibility libraries to poke through the application's user interface. We strive to help in building a quality desktop.
BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.
James (a.k.a Java Apache Mail Enterprise Server) is a 100% pure Java SMTP and POP3 Mail server, and NNTP News server designed to be a complete and portable enterprise mail/messaging engine solution based on currently available open messaging protocols.
PANTHER project: software for modeling of protein sequence and function evolution, and tools for applying these data to the analysis of genome data, expression data and coding SNPs. Details available at http://www.pantherdb.org.
Biskit is a python library for structural bioinformatics research. It simplifies the analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories and offers a platform for the rapid integration of external programs.