dna-bison
Bisulfite alignment On Nodes of a cluster
...Multiple compute nodes are not absolutely required, but will make the alignment process faster.
Further details available on the Wiki page. Help also available on SEQanswers (http://seqanswers.com/forums/showthread.php?t=31314) or by creating a ticket here.
You can now track the development on github (https://github.com/dpryan79/bison).
There is now a tutorial available in the downloads here: http://sourceforge.net/projects/dna-bison/files/bison_tutorial.tar.gz/download .