Bioinformatics: Tools

Written in C, it has a fast optimization algorithm (cached kernel evaluations, working set selection based on steepest feasible descent, and other optimizations). It can handle thousands of support vectors and several hundred thousand training examples. It supports the standard kernels, as well as letting users define their own kernel. Works on Linux, Cygwin, Solaris, Mac OS x, and Windows. Handles classification and regression problems, for multivariate and structured output use SVM-Struct.

Written both C++ and Java, but has interfaces with several languages, including Haskell, Ruby, Perl, MATLAB, .NET, Python, and others. It is a very general SVM solver: it tackles C-SVC, nu-SVC, epsilon-SVR, nu-SVR and distribution estimation problems. It can also handle multiclass classification. It includes standard kernels, as well as allowing the user to specify their own kernel. Its main features are cross validation for model selection (which can be automatic), weighted SVMs for unbalance.

According to its website, "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."

Includes tutorials, references, and software that can be plugged into MATLAB, as well as stand-alone.

According to the website, GROMACS is primarily designed to "simulate the Newtonian equations of motion for systems with hundreds to millions of particles." It is very optimized and is under plans of extension to even greater functionality.

According to its wiki, it is an "open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parses for common file formats, and allows the manipulation of sequences and 3D structures."

Holds many libraries that can also be found in CPAN. However, Bioperl includes plenty of reference and accessible assistance.

Contains a massive amount of libraries dedicated to efficient numerical processing.

EBI's massive index of tools in protein classification, sequence analysis, microarray analysis, structural and functional analysis, and many others.