The UMDHMM: Hidden Markov Model Toolkit is a free UNIX implementation of hidden Markov models useful for speech recognition from Tapas Kanungo. It includes implementations of the Forward-Backward, Viterbi and Baum-Welch algorithms.

TATOO (ISSCO Tagger Tool) is a free, trainable text part-of-speech tagger based on hidden Markov models offered by the ISSCO in Geneva. It was developed in the 1990s and is still available for download.

Siena (Simulation Investigation for Empirical Network Analysis) is a free program for statistical analysis developed particularly to work with social network data, but also applicable to other forms of network data. It models network dynamics via Markov chain models; this approach is best applied to data where relations between actors and their behaviour can be treated as a state rather than as an event. Siena's statistical analysis processes can be time-consuming, as the system works via computer simulation of the network. It was in continuous development from 2001 through 2010, releasing versions up to 3.2. Development on Siena as a stand-alone program has concuded, and the project has shifted focus to RSiena, a version of Siena deployed in R.

RSiena is a free, open source social network analysis package for R. It replaces Siena (Simulation Investigation for Empirical Network Analysis), which was a stand-alone program for Windows. Like its predecessor, RSiena is optimized for social network data, but is also applicable to other forms of network data, and relies on Markov chain models to generate network dynamics. This approach is best applied to data where relations between actors and their behaviour can be treated as a state rather than as an event. Users not familiar with R can run RSiena via the provided graphical user interface.