This is the download page for Handel[1], a Bayesian multiple alignment package based on Thorne, Kishino and Felsenstein's single-residue indel process[2].
Handel is now distributed as part of the DART package, available from SourceForge.
Preprint of Bioinformatics paper .ps (553K), .ps.gz (160K), .pdf (329K)
[1] 2001. Holmes I & Bruno WJ. Evolutionary HMMs: A Bayesian Approach to Multiple Alignment. Bioinformatics 17(9), 803-820. .ps .ps.gz .pdf
[2] 1991. Thorne JL, Kishino H & Felsenstein J. An Evolutionary Model for Maximum Likelihood Alignment of DNA Sequences. Journal of Molecular Evolution 33, 114-124.