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]

A software package to discover motifs (highly conserved regions) in groups of related DNA or protein sequences and, search sequence databases using motifs. [Commercial]

A library of tools for constructing maximum entropy (maxent) model in either python or C++. Some program features are L-BFGS and GIS parameter estimation, and gaussian prior smoothing. [GPL]

A Markov Logic Interpreter that focuses on efficient MAP inference and Online Learning featuring MAP inference using Cutting Planes combined with Max-Walk-Sat programming, parametrized weights, a shell interpreter, and cardinality constraints. [GPL]

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]

Various classes, packages, macros and other software systems related to machine learning. [GPL]

FTP repository of common list algorithms and datasets for research. [GPL]

Machine language tools including inductive systems (i.e. ILP and others), and other ML related links.

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]

Downloadable group of programs comprising the EMERALD machine learning system, (Experimental Machine Example-based Reasoning and Learning Disciple) integrates five modules (e.g. or 'robots'), each displaying a capability for machine learning, visualiz...