Software

Microbiome Analysis
MEGAN

MEGAN (“MEtaGenome ANalyzer”) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.

Metasim

Metasim is a sequencing simulator for genomes and metagenomes. This software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets.

Molecular modeling
BALLRapid Software Prototyping can significantly reduce development times in the field of Computational Molecular Biology and Molecular Modeling. BALL is an application framework in C++ that has been specifically designed for this purpose. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.
BALLViewBALLView is a fully featured stand-alone application for molecular visualization and molecular modeling. Whether you just want to look at protein structures or want to minimize structures with AMBER or CHARMM force fields, this is the way to do it. Available under the GNU Public License (GPL) for most platforms, inlcuding Linux, Windows, and MacOS.
Phylogenetics
Splitstree4

The leading application for computing unrooted phylogenetic networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks.

Dendroscope

An interactive viewer for large phylogenetic trees and networks.

Proteomics
OpenMSOpenMS is an open-source software C++ library for LC/MS data management and analyses. It offers an infrastructure for the development of mass spectrometry related software.
Systems biology
BN++

BN++ (formerly known as 'BioMiner') is a software system in C++ for analyzing and visualizing complex biochemical networks and processes. BN++ was designed to simplify the implementation of tools for answering a broad range of interesting biochemical questions. BN++ is based on a new comprehensive, extensible and reusable data model capable of representing complex and diverse biochemical data in a unified fashion.

FRED

FRED is a framework for T-cell epitope detection that offers consistent, easy, and simultaneous access to well established prediction methods for MHC binding and antigen processing. FRED can handle polymorphic proteins and offers analysis tools to combine, benchmark, or compare different methods. It is implemented in Python in a modular way and can easily be extended by user defined methods.

MayDay

Mayday is a workbench for visualization, analysis and storage of microarray data