(H)HMM Library and Designer
   This library allows probabilistic sequence models to be constructed through use of Hidden Markov models (HMMs) and Hierarchical Markov models HMMs (HHMMs) in Ocaml programming language. [GPL]
   http://connex.lip6.fr/%7ebinsztok/hhld.html

ArrayMiner - ClassMarker
   Programmatically isolate similarities between scattered classes of genes. Expression driven. Utilizes a voting method along with a k-Nearest-Neighbors classification. Very rich graphical interface. Samples of an unknown class are possible given enough
   http://www.optimaldesign.com/ArrayMiner/ClassMarker.htm

BETSY: A Bayesian Essay Test Scoring System
   A windows-based program that classifies text based on trained material. Designed for automated essay scoring, BETSY can be applied to any text classification task. [GPL]
   http://edres.org/betsy

BNET, Belief Network Tools & VisionKit, Computer Vision Components
   A developer toolkit for researchers and engineers to embed belief networks in software applications. Nice online demo. [Commercial]
   http://www.cra.com/commercial-products-services/bnet-engine-kit.asp

Bayes Net Toolbox for Matlab
   Supports several inference algorithms and learning algorithms. Allows simulation of static and dynamic networks, including HMMs, IOHMMs, and Kalman filters. [GPL]
   http://bnt.sourceforge.net/

Bayes++: Open Source Bayesian Filtering Classes
   A library of C++ classes for Bayesian Filtering of discrete systems. [MIT]
   http://bayesclasses.sourceforge.net/Bayes++.html

BayesBuilder: Bayesian network construction tool
   This tool supports discrete gaussians and efficient noisy-OR nodes necessary in large networks. Node search, undo/redo, and automatic network layout are also supported. Written in C++ with a Java front end. [GPL]
   http://www.snn.ru.nl/nijmegen/index.php3?page=31

Bow: A Toolkit for Statistical Language Modeling, Text Retrieval, Classification and Clustering
   A library of C code useful for writing statistical text analysis, language modeling, and information retrieval programs. The current distribution includes the library, as well as front-ends for document classification (rainbow), document retrieval (arrow)
   http://www.cs.cmu.edu/~mccallum/bow/

C4.5 and FOIL
   The home page of R. Quinlan with FTP links to FOIL (inductive logic programming) and C4.5 (learning decision trees). [LGPL]
   http://www.rulequest.com/Personal/

CHILL: Constructive Heuristics Induction for Language Learning
   A general approach to the problem of inducing natural language parsers. It uses an annotated corpus, and produces a parser by using ILP for inducing the rules that control the actions of a shift-reduce parser. [Free]
   http://www.cs.utexas.edu/users/ml/chill.html

Classification Toolbox for MATLAB
   A complete set of algorithms for classification, clustering, feature selection and reduction for Matlab. [Free]
   http://www.yom-tov.info/toolbox.html

Data Access Tools from the US Census Bureau
   General purpose data display and extraction tools that works with Census Bureau data. Census data available for pickup through census bureau employees only. [Free]
   http://www.census.gov/main/www/access.html

ELIE: An Adaptive Information Extraction System
   A tool for adaptive information extraction from text. Also included are a number of other text processing tools for POS tagging, chunking, gazetteer, and stemming. [GPL]
   http://www.aidanf.net/software/elie_an_adaptive_information_extraction_system

Experience-based Language Acquisition
   Computational model of human language acquisition written in Java; currently acquires a protolanguage of nouns and verbs language based on visual perception. [BSD]
   http://sourceforge.net/projects/ebla

FTP Repository Site List for Cognitive and Machine Learning
   Anonymous sites from popular colleges and universities. To access other pages just replace the 6 in URL with numbers 1-23. [Free]
   http://hoohoo.ncsa.uiuc.edu/ftp/part6.html

FastMix
   Generates Gaussian mixture models for large datasets using efficient KD-clustering algorithms. [Free]
   http://www.cs.cmu.edu/~psand/

GAlib: Matthew's Genetic Algorithms Library
   A toolset of genetic algorithm objects for C++ to perform optimization. Uses any representation and genetic operators. The documentation contains implementation and examples. Nice screenshots. PVM for distributed, parallel implementations. Includ
   http://lancet.mit.edu/ga/

GRIDLOCK: A Scalable Approach to Unifying Computer and Communications Security
   A globally specified and locally interpreted policy language based software for specification of network access control policy. [GPL]
   http://nsl.cs.columbia.edu/projects/gridlock/

General Hidden Markov Model Library
   Hidden Markov Models software library from the Center of Applied Informatics, Cologne. Includes algorithms such as Viterbi, Baum-Welch, and Forward-Backward. [GPL]
   http://sourceforge.net/projects/ghmm

HMM and other statistical programs
   This tool implements Hidden Markov Models and application to part-of-speech tagging. Also available; a multivariate hypothesis testing software for gaussian data, and a groundtruth/metadata editing and visualizing toolkit for OCR. [GPL]
   http://www.kanungo.com/software/software.html

HMMER: Biosequence Analysis
   A tool used to build HMMs from multiple alignments and calculate e-scores. [GPL]
   http://hmmer.janelia.org/

HRE API: A Portable Handwriting Recognition Engine
   This engine is a functionally complete interface for handwriting recognition. API was written in ANSI C and has minimal reliance on the Windows system. There is a version ported to Linux. [GPL]
   http://playground.sun.com/pub/multimedia/handwriting/hre.html

ITI: Incremental Tree Inducer
   An algorithm that incrementally constructs decision trees from labeled examples. [AFL]
   http://www.cs.umass.edu/~lrn/iti/index.html

KEEL: Knowledge Extraction based on Evolutionary Learning
   The aim of this project is to develop a Computational Environment for integrating the design and use of knowledge extraction models from data using evolutionary algorithms. Genetic learning may also be applied to the model. [GPL]
   http://sci2s.ugr.es/keel/

Lemga: Learning Models and Generic Algorithms
   A library of classes for optimizing (training) the generic models. Written in C++. [GPL]
   http://www.work.caltech.edu/ling/lemga/

LingPipe: Natural Language Processor (NLP)
   A suite of Java libraries for the linguistic analysis of human language which can link entity mentions to database entries, uncover relations, cluster documents, and discover significant trends. [GPL]
   http://www.alias-i.com/lingpipe/

MALLET: Advanced Machine Learning for Language
   An integrated collection of Java code useful for statistical natural language processing, document classification, clustering, information extraction, and other machine learning applications to text. [GPL]
   http://mallet.cs.umass.edu/index.php/Main_Page

MEME/MAST: Motif Discovery and Search
   A software package to discover motifs (highly conserved regions) in groups of related DNA or protein sequences and, search sequence databases using motifs. [Commercial]
   http://meme.sdsc.edu/meme/intro.html

MIX: Software for Mixture Distributions
   Software for learning mixture distributions. Examples and two case studies are included. [Commercial]
   http://icarus.math.mcmaster.ca/peter/mix/mix.html

Machine Learning Programs by Peter Clark
   A collection of downloadable packages including: KM - The Knowledge Machine, Guiding Inductive Learning with a Qualitative Model, LPE - Lazy Partial Evaluation, and CN2 - Rule induction from examples. [GPL]
   http://www.cs.utexas.edu/users/pclark/software/

Machine Learning Research Software in LISP
   FTP repository of common list algorithms and datasets for research. [GPL]
   http://www.cs.utexas.edu/~ml/ml-progs.html

Machine Learning Software Packages
   FTP software repository of machine learning programs from Carnegie Mellon University School of Computer Science. There are also links to other repositories. [GPL]
   http://www.cs.cmu.edu/afs/cs/project/ai-repository/ai/areas/learning/systems/0.html

Maximum Entropy Modeling Toolkit
   A library of tools for constructing maximum entropy (maxent) model in either python or C++. Some program features are L-BFGS & GIS parameter estimation, and gaussian prior smoothing. [GPL]
   http://homepages.inf.ed.ac.uk/s0450736/maxent_toolkit.html

Meta-MEME: Motif-based Hidden markov Modeling of Biological Sequences
   Software toolkit for building and using motif-based hidden Markov models of DNA and proteins. There is an online interactive version. Source written in C. [GPL]
   http://metameme.sdsc.edu/

Monkiefarm: A Genetic Algorithm Library
   This toolset uses an easily extensible genetic graph bipartitioning algorithm to run over an NP hard problem. It encompasses multi-layer perceptron implementations, written in C++. [GPL]
   http://allies.freezope.org/html/index.html

NEITHER: A Propositional Theory Refinement
   A system to modify an incomplete or incorrect rule base to make it consistent with a set of input training examples. Written in C++ [Free]
   http://www.cs.utexas.edu/users/ml/neither.html

NSP: N-gram Statistics Package
   Software for counting and analyzing word n-grams in text. This package provides standard tests of association for identifying word n-grams in large corpora and allows users to implement other tests with minimal scripting knowledge. Written in Perl. [GP
   http://www.d.umn.edu/~tpederse/nsp.html

New Scientific Brainstorming Software for Inventors -- Windows, Mac and Linux
   A software developed to help your team brainstorm. Words are replaced programmatically in user's idea sentence with new words from program categories perhaps creating ideas not formerly thought of. Extensive word categories. [Commercial]
   http://www.paramind.net/pmscientificversion.html

Nieme Machine Learning Library
   Nieme is a Machine Learning library for classification, regression and ranking. It implements several well-known algorithms and is specially designed for large-scale applications.
   http://www-connex.lip6.fr/%7emaes/wikihomepage/pmwiki.php?n=Nieme.Nieme

Nonparametric Classification with Polynomial MPMC Cascades
   Scalable non-parametric classification with Polynomial MPMC Cascades for use in Matlab. [GPL]
   http://cervisia.org/machine_learning_code.php

ORANGE: Inter-active Machine Learning Data Mining components
   A component based framework for data input/output, preprocessing, predictive modelling, ensemble methods, and modelling validation. [GPL]
   http://www.ailab.si/orange

OpenCyc
   Open source version of the Cyc technology, the world's largest and most complete general knowledge base and commonsense reasoning engine. Can be used as the basis of a wide variety of intelligent applications including; rapid development of an ontology
   http://www.opencyc.org/

PRAPI: Pattern Recognition Application Programmer's Interface
   A library for many pattern recognition tasks. The main focus of this package is on image analysis but utilizes a general architecture and XML-based data interchange format. Written in C++ [GPL]
   http://www.ee.oulu.fi/~topiolli/cppdocs/

PRODIGY: An Architecture for Planning and Learning
   A system of research planning and learning utilizing explanation-based learning, partial evaluation, experimentation, graphical knowledge acquisition, automatic abstraction, mixed-initiative planning, and case-based reasoning. [Free]
   http://www.cs.cmu.edu/afs/cs.cmu.edu/project/prodigy/Web/prodigy-home.html

Pattern Matching Pointers
   Using algorithms to address issues of searching and matching strings and more complicated patterns such as trees, regular expressions, graphs, point sets, and arrays. [GPL]
   http://www.cs.ucr.edu/~stelo/pattern.html

Pfam: Database of Protein Families and HMMs
   A large collection of multiple sequence alignments and trained hidden Markov models covering many common protein domains. Alignments are included as well as models for 8296 protein families, based on the Swissprot 48.9 and SP-TrEMBL 31.9 protein sequence
   http://pfam.wustl.edu/

Probabilistic Networks Library (PNL), and Open Source Machine Learning Library (OpenML) by Intel
   Open source library of tools for building machine learning software based on Bayesian mathematical principles. Links on lower left of page article. [GPL]
   http://deviceforge.com/news/NS5332804106.html

SAM: Sequence Alignment and Modeling
   A collection of tools for creating and using HMMs for biological sequences. [AFL]
   http://bioweb.pasteur.fr/seqanal/motif/sam-uk.html

SNoW: Sparse Network of Winnows
   A learning architecture specifically tailored for learning in very high-dimensional feature spaces. The current release uses sparse variations of Winnow, Perceptron, and Naive Bayes. [AFL]
   http://l2r.cs.uiuc.edu/~danr/snow.html

SUBDUE: Graph Based Knowledge Discovery
   A program which discovers interesting and repetitive subgraphs in labeled graph representations using the minimum description length principle. Includes applications to molecular biology. [Free]
   http://cygnus.uta.edu/subdue/

SenseClusters
   Programs to cluster similar contexts together using unsupervised knowledge-lean methods for word sense discrimination, email categorization, and name discrimination. Written in Perl. [GNU]
   http://senseclusters.sourceforge.net/

Software Packages and Toolboxes
   Online software repository of the Department of Computer Science at The University of Pittsburg. Everything from expert systems, finite-state machines, graphical models, linear programming, and machine learning through turning machines is covered here an
   http://www.isp.pitt.edu/information/software.html

Software Packages for Graphical Models/Bayesian Networks
   Tools for modeling graphs & Bayesian networks. Scroll down. [AFL], [Commercial]
   http://www.ai.mit.edu/~murphyk/Software/bnsoft.html

Sorting Algorithms for Machine Learning
   Various sorting algorithms including insertion, quick, merge, heap, Dutch National Flag, and radix with on-line demos. [Free]
   http://www.csse.monash.edu.au/%7Elloyd/tildeAlgDS/Sort/

Spider: General Purpose Machine Learning Toolbox in Matlab
   An object orientated environment for machine learning in Matlab. Algorithms can be plugged together and can be compared with (e.g. model selection, statistical tests and visual plots). Algorithms may be downloaded separately. [GPL]
   http://www.kyb.tuebingen.mpg.de/bs/people/spider/index.html

TIMBL: Tilburg Memory Based Learner
   A program implementing several memory-based learning techniques. These learners store representation of the training set explicitly, and classifies new cases by extrapolation from the most similar stored cases. [AFL]
   http://ilk.uvt.nl/software.html

The AutoClass Project
   A database of cases described by a combination of real and discrete valued attributes, and automatically finds the natural classes in that data. It can be seen as a Naive Bayes classifier where the class node is hidden. [Free]
   http://ic-www.arc.nasa.gov/ic/projects/bayes-group/autoclass/

The Observable Operator Modeling Kit
   Machine learning library for 'observable operator models' (OOMs) suitable for time-series and sequence data classification and prediction. OOMs are similar but more powerful than HMMs. Written in C++ [BSD]
   http://omk.sourceforge.net

The PNC2 Rule Induction System
   Windows software tool that induces rules from your data using the PNC2 cluster algorithm. An integrated parameter-tuning component allows easy adjustment of the algorithms behavior to the given problem without requiring any further knowledge. [GPL]
   http://www.newty.de/pnc2/index.html

The Torch Machine Learning Library
   This package forms a complete gradient descent machine learning library. Modules support vector machines in classification and regression, ensemble models such as bagging or adaboost, non-parametric models such as K-nearest neighbors, Parzen regression,
   http://www.torch.ch

Tree Visualizer
   Software which allows one to navigate (fly) through the data tree, zoom in on interesting nodes, click on bars to get counts, and mark interesting places in the tree. Includes datasets for automobiles, voting, produce, and medical research. Uses LEDA, (
   http://www.sgi.com/tech/mlc/trees.html

UCI Machine Learning Repository
   A repository of databases, domain theories and data generators that are used by the machine learning community for the empirical analysis of machine learning algorithms at the University of California at Irvine. [Free]
   http://www.ics.uci.edu/~mlearn/MLRepository.html

VIBES: Variational Inference for Bayesian Networks
   A software package which allows variance-modeled posterior inference to be performed automatically on a Bayesian network. [GPL]
   http://vibes.sourceforge.net/

WebMO
   Web-based interface to computational chemistry. Has support for Gaussian 94/98/03, GAMESS, MolPro 2002, MOPAC 7/93/200x, NWChem 4.6+, QChem 2.1+, and Tinker 4.2+. Unix or Linux based. [Free]
   http://www.webmo.net/

Weka 3: Data Mining Software
   A collection of tools that implement decision trees and tables, rule learners, Naive Bayes, support vector machines, voted perceptrons, multi-layer perceptron. Meta schemes include bagging, stacking, and boosting. Written in Java. [GPL]
   http://www.cs.waikato.ac.nz/~ml/weka/index.html

What If: Web-based Scientific Discovery
   An algorithm engine which will calculate everything from symmetry, torsion angles, polar fraction through protein analysis and bond angles. Online version only. [Free]
   http://swift.cmbi.kun.nl/WIWWWI/

WinBUGS: The BUGS Project
   A stand-alone program to allow practical MCMC methods available to applied statisticians. Either a point and click interface can be used to control the analysis or a graphical interface can be constructed. The BUGs project also includes links to GeoBUG
   http://www.mrc-bsu.cam.ac.uk/bugs/winbugs/contents.shtml

WinMine Toolkit
   A set of tools for Windows 2000/NT/XP that allow you to build statistical models from data. [Free]
   http://research.microsoft.com/~dmax/WinMine/tooldoc.htm

YaLE: Yet another Learning Environment
   The YALE toolset is an environment for machine learning through use of nested operators. Multiple experiments can be arbitrarily nested together through use of a graphical XML based user interface. [GPL]
   http://rapid-i.com/

libbpfl - A Bayesian Probability Filtering Library
   A general purpose library for Bayesian filtering written in C++. [LGPL]
   http://libbpfl.sourceforge.net