FAST (Fourier transform based Algorithms for Significance Testing of ungapped multiple alignments) is an open-source C/C++ package
of programs and associated libraries for evaluating ungapped multiple alignments. The details of the package are described in an
accompanying paper (currently in submission).
The FAST package is available for download here: fast.tar.gz.
A webserver for some of the programs in the package is also available
here.
For questions and suggestions contact: niranjan at umiacs.umd.edu