"A Sound-Change Applier" is relatively user-friendly, Unicode-aware command-line tool for applying sound changes to word lists. It is implemented in Java and supports a naturalistic human-readable rule format, and permits the definition of sets and variables within the rules file. It also has limited support for Kleene-star-like operators.
I am currently rewriting the code-base of the program in order to improve its handling of diacritics and to enable support for default or user-defined feature systems.
The Multilingual Cognate Alignment System is a computational framework for generating lists of sounds correspondences between cognate material in any number of related languages. MCAS accomplishes this by using a dynamic programming techinique loosely based on the Smith-Waterman algorithm used in DNA and protein sequence alignment, but operates in an n-dimensional number space. Scoring is performed using a numerical model of phonetic features based on articulatory and perceptual properties.