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Ear-Training / Fundamentals
Online Rudiments Drills
Robert Whelan has created a collection of drills that anyone with a Java-enabled browser can use online. Right now there are modules for clef-reading, intervals, scales, and chords. Most online activities I've looked at are useless, hideous contraptions - Whelan's work is the brilliant exception to the rule. My one caveat is that some of the programs are not set up to do immediate, intelligent practice - one must go into the "options" menu to configure what you want to work on.
A web-based ear-training driller. Looks OK. I couldn't get the embedded quicktime clips to work with my Firefox browser, but they displayed fine in Internet Explorer.
GNU Solfege
A fairly thorough ear training program, including drills on intervals, chords, rhythms, and even a simple interface for dictation. (It will play an excerpt, then show the answer.) It is written to be usable on multiple platforms (Linux et al.) and thus it will appear a little strange to the average Windows consumer.
Take Note 2.12 by Jon L. Jacobi
This is an old commercial product that has gone free. It drills pitches, intervals, scales, chords, and rhythms, using both eye and ear. It’s fairly difficult to get started with it thanks to a clunky interface. It does feature one stroke of genius, however, a three-paned display that represents notes simultaneously on a grand staff, piano keyboard, and guitar fretboard.
I am also working on a text-based rudiments program.
Atonal Theory Tools
PCN2001 by Jamary Oliveira
A neat-looking set-class calculator with a broad assortment of functions. This latest version can even take input from a MIDI keyboard.
SetMaker and pSetMaker by Michael Buchler
A command-line program for exploring pc sets. Gives very detailed info on the properties of a set, with options to explore subsets, supersets, combination, similarity and transformations. Among the programs in a similar format (mod12, AthenaCL) I’d recommend starting here. The program includes some terse documentation, and one could presumably learn much more about its output from Buchler’s dissertation (also available on the site.) pSetMaker is a similar tool that explores sets of pitches (as opposed to pitch-classes.)
AthenaCL by Christopher Ariza
A monster application. Ariza seems to have started with a command-line utility for making his own algorhythmic compositions, but then he packed it with all kinds of analytic measures. AthenaCL can give lots of set-class information, do similarity measures, and even explore voice-leading possibilities between sets (drawing on recent work by Joseph Straus). Somehow this data can be assembled into a score or even an audio file via CSound. This program is written in the “python” language, and is therefore functional on many platforms including PC and Mac. You must install python (at www.python.org) before installing AthenaCL.
mod12 by Thomas Demske
MS-DOS program. Could be used as a simple set calculator. For those with patience and some programming skills it could be used for advanced set research.
Larry Solomon’s Music Analysis System
Explores the inter-relations of a group of set-classes.
WinSims by Eric Isaacson
Can give 30 different measures for the similarity between two sets, “including similarity relations by Forte, Alphonse, Teitelbaum, Lord, Morris, Rahn, Lewin, Castren, and Isaacson…”
And of course there is my own Post-Tonal Ear-Training Suite

Research and Advanced Topics
Scala by Manuel Op de Coul
Fascinating. Can create, examine, and play microtonal scales. It can even adapt existing MIDI files to a microtonal system.

Last updated 10/6/08 by Dave Smey. Please email me with new links, comments, questions.
(Thanks to Michael Buchler for links.)